@article{2-s2.0-85152122972,

title = {Characterization of meiotic chromosome behavior in the autopolyploid Saccharum spontaneum reveals preferential chromosome pairing without distinct DNA sequence variation},

author = { Xi. Zhang and Z. Meng and J. Han and H. Khurshid and A.M.H. Esh and R. Hasterok and K. Wang},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85152122972&doi=10.1016%2fj.cj.2023.02.008&partnerID=40&md5=466992e43ea72fa564f22aa149f40ffd},

doi = {10.1016/j.cj.2023.02.008},

issn = {20955421},

year  = {2023},

date = {2023-01-01},

journal = {Crop Journal},

volume = {11},

number = {5},

pages = {1550-1558},

publisher = {KeAi Communications Co.},

abstract = {Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy, and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide (oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization (FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I (MI) in autotetraploid, autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploidized chromosome behavior; so that homologous chromosomes formed almost exclusively bivalents during MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants. © 2023 Crop Science Society of China and Institute of Crop Science, CAAS},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85150956277,

title = {Characterization of centromeric DNA of Gossypium anomalum reveals sequence-independent enrichment dynamics of centromeric repeats},

author = { W. Ding and Yu. Zhu and J. Han and Ha. Zhang and Zh. Xu and H. Khurshid and Fe. Liu and R. Hasterok and X. Shen and K. Wang},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85150956277&doi=10.1007%2fs10577-023-09721-z&partnerID=40&md5=1ce0ede37be28d5d12ddcefe7983b482},

doi = {10.1007/s10577-023-09721-z},

issn = {09673849},

year  = {2023},

date = {2023-01-01},

journal = {Chromosome Research},

volume = {31},

number = {2},

publisher = {Institute for Ionics},

abstract = {Centromeres in eukaryotes are composed of highly repetitive DNAs, which evolve rapidly and are thought to achieve a favorable structure in mature centromeres. However, how the centromeric repeat evolves into an adaptive structure is largely unknown. We characterized the centromeric sequences of Gossypium anomalum through chromatin immunoprecipitation against CENH3 antibodies. We revealed that the G. anomalum centromeres contained only retrotransposon-like repeats but were depleted in long arrays of satellites. These retrotransposon-like centromeric repeats were present in the African–Asian and Australian lineage species, suggesting that they might have arisen in the common ancestor of these diploid species. Intriguingly, we observed a substantial increase and decrease in copy numbers among African–Asian and Australian lineages, respectively, for the retrotransposon-derived centromeric repeats without apparent structure or sequence variation in cotton. This result indicates that the sequence content is not a decisive aspect of the adaptive evolution of centromeric repeats or at least retrotransposon-like centromeric repeats. In addition, two active genes with potential roles in gametogenesis or flowering were identified in CENH3 nucleosome-binding regions. Our results provide new insights into the constitution of centromeric repetitive DNA and the adaptive evolution of centromeric repeats in plants. © 2023, The Author(s), under exclusive licence to Springer Nature B.V.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85148741328,

title = {Switch them off or not: selective rRNA gene repression in grasses},

author = { N. Borowska-Zuchowska and S. Mykhailyk and E. Robaszkiewicz and N. Matysiak and Ł. Mielańczyk and R. Wojnicz and A. Kovaík and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85148741328&doi=10.1016%2fj.tplants.2023.01.002&partnerID=40&md5=6e1efd90c31d10c0fed768f36099193f},

doi = {10.1016/j.tplants.2023.01.002},

issn = {13601385},

year  = {2023},

date = {2023-01-01},

journal = {Trends in Plant Science},

volume = {28},

number = {6},

pages = {661-672},

publisher = {Elsevier Ltd},

abstract = {Nucleolar dominance (ND) is selective epigenetic silencing of 35-48S rDNA loci. In allopolyploids, it is frequently manifested at the cytogenetic level by the inactivation of nucleolar organiser region(s) (NORs) inherited from one or several evolutionary ancestors. Grasses are ecologically and economically one of the most important land plant groups, which have frequently evolved through hybridisation and polyploidisation events. Here we review common and unique features of ND phenomena in this monocot family from cytogenetic, molecular, and genomic perspectives. We highlight recent advances achieved by using an allotetraploid model grass, Brachypodium hybridum, where ND commonly occurs at a population level, and we cover modern genomic approaches that decipher structural features of core arrays of NORs. © 2023 The Author(s)},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85144754728,

title = {Erratum: Brachypodium: 20 years as a grass biology model system; the way forward?: (Trends in Plant Science 27, 1002-1016, 2022) (Trends in plant science (2022) 27 10 (1002-1016) PII: S1360-1385(22)00308-9)},

author = { R. Hasterok and P. Catalán and S.P. Hazen and A.C. Roulin and J.P. Vogel and Ka. Wang and L.A.J. Mur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85144754728&doi=10.1016%2fj.tplants.2022.12.001&partnerID=40&md5=675668ddfc849910d8e1babe4bf1d2d3},

doi = {10.1016/j.tplants.2022.12.001},

issn = {18784372},

year  = {2023},

date = {2023-01-01},

journal = {Trends in plant science},

volume = {28},

number = {2},

pages = {252-253},

publisher = {NLM (Medline)},

abstract = {[No abstract available]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85141816221,

title = {Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium},

author = { V.T. Scarlett and J.T. Lovell and M. Shao and J.L. Phillips and S. Shu and J. Lusinska and D. Goodstein and J. Jenkins and J. Grimwood and K. Barry and B. Chalhoub and J. Schmutz and R. Hasterok and P. Catalán and J.P. Vogel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141816221&doi=10.1093%2fgenetics%2fiyac146&partnerID=40&md5=85eab2c1ad8cab594ff75aa810fbb34e},

doi = {10.1093/genetics/iyac146},

issn = {00166731},

year  = {2023},

date = {2023-01-01},

journal = {Genetics},

volume = {223},

number = {2},

publisher = {Oxford University Press},

abstract = {The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession “Bhyb26.” We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance. © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85139931114,

title = {The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae)},

author = { G. Yücel and A. Betekhtin and E. CabI and M. Tuna and R. Hasterok and B.A. Kolano},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85139931114&doi=10.3390%2fijms231911033&partnerID=40&md5=420940d23056c306f8913a2a35f4204e},

doi = {10.3390/ijms231911033},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {19},

publisher = {MDPI},

abstract = {The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85130917166,

title = {Brachypodium: 20 years as a grass biology model system; the way forward?},

author = { R. Hasterok and P. Catalán and S.P. Hazen and A.C. Roulin and J.P. Vogel and K. Wang and L.A.J. Mur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130917166&doi=10.1016%2fj.tplants.2022.04.008&partnerID=40&md5=ecb36a40f55b3a4c0dd055efad1ebce9},

doi = {10.1016/j.tplants.2022.04.008},

issn = {13601385},

year  = {2022},

date = {2022-01-01},

journal = {Trends in Plant Science},

volume = {27},

number = {10},

pages = {1002-1016},

publisher = {Elsevier Ltd},

abstract = {It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress. © 2022 The Author(s)},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85130260970,

title = {Corrigendum: To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum (Front. Plant Sci., (2021), 12, (768347), 10.3389/fpls.2021.768347)},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and S. Mykhailyk and J. Wartini and A. Piński and A. Kovaík and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85130260970&doi=10.3389%2ffpls.2022.917940&partnerID=40&md5=9b0bae9c81633dfeba911097fe74aa37},

doi = {10.3389/fpls.2022.917940},

issn = {1664462X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Plant Science},

volume = {13},

publisher = {Frontiers Media S.A.},

abstract = {In the original article, there was a mistake in Figure 3B as published. The gel lines were marked in an incorrect order. The corrected Figure 3B appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. Copyright © 2022, Borowska-Zuchowska, Robaszkiewicz, Mykhailyk, Wartini, Pinski, Kovarik and Hasterok.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85124541947,

title = {Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids},

author = { R. Sancho and L.A. Inda and A. Díaz-Pérez and D.L. Des Marais and S.P. Gordon and J.P. Vogel and J. Lusinska and R. Hasterok and B. Contreras-Moreira and P. Catalán},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124541947&doi=10.1111%2ftpj.15650&partnerID=40&md5=6f5bd8cc89b48838d1305be677f5be4d},

doi = {10.1111/tpj.15650},

issn = {09607412},

year  = {2022},

date = {2022-01-01},

journal = {Plant Journal},

volume = {109},

number = {6},

pages = {1535-1558},

publisher = {John Wiley and Sons Inc},

abstract = {[No abstract available]},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85116985663,

title = {Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes},

author = { C. Stritt and E.L. Gimmi and M. Wyler and A.H. Bakali and A. Skalska and R. Hasterok and L.A.J. Mur and N. Pecchioni and A.C. Roulin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85116985663&doi=10.1111%2fmec.16207&partnerID=40&md5=6b239013be251a1b2ce6ebee8d953a24},

doi = {10.1111/mec.16207},

issn = {09621083},

year  = {2022},

date = {2022-01-01},

journal = {Molecular Ecology},

volume = {31},

number = {1},

pages = {70-85},

publisher = {John Wiley and Sons Inc},

abstract = {Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics – and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. A total of 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species. © 2021 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121989036,

title = {To Be or Not to Be Expressed: The First Evidence of a Nucleolar Dominance Tissue-Specificity in Brachypodium hybridum},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and S. Mykhailyk and J. Wartini and A. Piński and A. Kovaík and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121989036&doi=10.3389%2ffpls.2021.768347&partnerID=40&md5=ef4ed95412d5b77ca61c65fd3acb3f58},

doi = {10.3389/fpls.2021.768347},

issn = {1664462X},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Plant Science},

volume = {12},

publisher = {Frontiers Media S.A.},

abstract = {Nucleolar dominance (ND) is an epigenetic, developmentally regulated phenomenon that describes the selective inactivation of 35S rDNA loci derived from one progenitor of a hybrid or allopolyploid. The presence of ND was documented in an allotetraploid grass, Brachypodium hybridum (genome composition DDSS), which is a polyphyletic species that arose from crosses between two putative ancestors that resembled the modern B. distachyon (DD) and B. stacei (SS). In this work, we investigated the developmental stability of ND in B. hybridum genotype 3-7-2 and compared it with the reference genotype ABR113. We addressed the question of whether the ND is established in generative tissues such as pollen mother cells (PMC). We examined condensation of rDNA chromatin by fluorescence in situ hybridization employing state-of-art confocal microscopy. The transcription of rDNA homeologs was determined by reverse-transcription cleaved amplified polymorphic sequence analysis. In ABR113, the ND was stable in all tissues analyzed (primary and adventitious root; leaf; and spikes). In contrast, the 3-7-2 individuals showed a strong upregulation of the S-genome units in adventitious roots but not in other tissues. Microscopic analysis of the 3-7-2 PMCs revealed extensive decondensation of the D-genome loci and their association with the nucleolus in meiosis. As opposed, the S-genome loci were always highly condensed and localized outside the nucleolus. These results indicate that genotype-specific loss of ND in B. hybridum occurs probably after fertilization during developmental processes. This finding supports our view that B. hybridum is an attractive model to study ND in grasses. Copyright © 2021 Borowska-Zuchowska, Robaszkiewicz, Mykhailyk, Wartini, Pinski, Kovarik and Hasterok.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85110027459,

title = {3,4‐dehydro‐l‐proline induces programmed cell death in the roots of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and J. Kwaśniewska and Ł. Chajec and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85110027459&doi=10.3390%2fijms22147548&partnerID=40&md5=045642b6770419a71c99a63d6dd94f4c},

doi = {10.3390/ijms22147548},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {14},

publisher = {MDPI},

abstract = {As cell wall proteins, the hydroxyproline‐rich glycoproteins (HRGPs) take part in plant growth and various developmental processes. To fulfil their functions, HRGPs, extensins (EXTs) in particular, undergo the hydroxylation of proline by the prolyl‐4‐hydroxylases. The activity of these enzymes can be inhibited with 3,4‐dehydro‐L‐proline (3;4‐DHP), which enables its application to reveal the functions of the HRGPs. Thus, to study the involvement of HRGPs in the development of root hairs and roots, we treated seedlings of Brachypodium distachyon with 250 μM, 500 μM, and 750 μM of 3,4‐DHP. The histological observations showed that the root epidermis cells and the cortex cells beneath them ruptured. The immunostaining experiments using the JIM20 antibody, which recognizes the EXT epitopes, demonstrated the higher abundance of this epitope in the control compared to the treated samples. The transmission electron microscopy analyses revealed morphological and ultrastructural features that are typical for the vacuolar‐type of cell death. Using the TUNEL test (terminal deoxynucleotidyl transferase dUTP nick end labelling), we showed an increase in the number of nuclei with damaged DNA in the roots that had been treated with 3,4‐DHP compared to the control. Finally, an analysis of two metacaspases’ gene activity revealed an increase in their expression in the treated roots. Altogether, our results show that inhibiting the prolyl‐4‐hydroxyl-ases with 3,4‐DHP results in a vacuolar‐type of cell death in roots, thereby highlighting the important role of HRGPs in root hair development and root growth. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85108260977,

title = {Changes in the cell wall proteome of leaves in response to high temperature stress in brachypodium distachyon},

author = { A. Piński and A. Betekhtin and B. Skupien‐rabian and U. Jankowska and E. Jamet and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108260977&doi=10.3390%2fijms22136750&partnerID=40&md5=bd0c6a761d804c4e3473abb1174f406e},

doi = {10.3390/ijms22136750},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {13},

publisher = {MDPI},

abstract = {High temperature stress leads to complex changes to plant functionality, which affects, i.a., the cell wall structure and the cell wall protein composition. In this study, the qualitative and quantitative changes in the cell wall proteome of Brachypodium distachyon leaves in response to high (40 °C) temperature stress were characterised. Using a proteomic analysis, 1533 non‐redundant proteins were identified from which 338 cell wall proteins were distinguished. At a high temperature, we identified 46 differentially abundant proteins, and of these, 4 were over‐accumulated and 42 were under‐accumulated. The most significant changes were observed in the proteins acting on the cell wall polysaccharides, specifically, 2 over‐ and 12 under‐accumulated proteins. Based on the qualitative analysis, one cell wall protein was identified that was uniquely present at 40 °C but was absent in the control and 24 proteins that were present in the control but were absent at 40 °C. Overall, the changes in the cell wall proteome at 40 °C suggest a lower protease activity, lignification and an expansion of the cell wall. These results offer a new insight into the changes in the cell wall proteome in response to high temperature. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85102249208,

title = {The formation and evolution of centromeric satellite repeats in Saccharum species},

author = { Y. Huang and W. Ding and M. Zhang and J. Han and Y. Jing and W. Yao and R. Hasterok and Z. Wang and K. Wang},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102249208&doi=10.1111%2ftpj.15186&partnerID=40&md5=b7d5321b2965de2eb2eea22e93150747},

doi = {10.1111/tpj.15186},

issn = {09607412},

year  = {2021},

date = {2021-01-01},

journal = {Plant Journal},

volume = {106},

number = {3},

pages = {616-629},

publisher = {Blackwell Publishing Ltd},

abstract = {Centromeres in eukaryotes are composed of tandem DNAs and retrotransposons. However, centromeric repeats exhibit considerable diversity, even among closely related species, and their origin and evolution are largely unknown. We conducted a genome-wide characterization of the centromeric sequences in sugarcane (Saccharum officinarum). Four centromeric tandem repeat sequences, So1, So103, So137 and So119, were isolated. So1 has a monomeric length of 137 bp, typical of a centromeric satellite, and has evolved four variants. However, these So1 variants had distinct centromere distributions and some were unique to an individual centromere. The distributions of the So1 variants were unexpectedly consistent among the Saccharum species that had different basic chromosome numbers or ploidy levels, thus suggesting evolutionary stability for approximately 7 million years in sugarcane. So103, So137 and So119 had unusually longer monomeric lengths that ranged from 327 to 1371 bp and lacked translational phasing on the CENH3 nucleosomes. Moreover, So103, So137 and So119 seemed to be highly similar to retrotransposons, which suggests that they originated from these mobile elements. Notably, all three repeats were flanked by direct repeats, and formed extrachromosomal circular DNAs (eccDNAs). The presence of circular molecules for these retrotransposon-derived centromeric satellites suggests an eccDNA-mediated centromeric satellite formation pathway in sugarcane. © 2021 Society for Experimental Biology and John Wiley & Sons Ltd},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85103919767,

title = {Metabolomic variation aligns with two geographically distinct subpopulations of Brachypodium distachyon before and after drought stress},

author = { A. Skalska and M. Beckmann and F. Corke and G.S. Tuna and M. Tuna and J.H. Doonan and R. Hasterok and L.A.J. Mur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85103919767&doi=10.3390%2fcells10030683&partnerID=40&md5=a9030ff843ea928e01952948c2642bbc},

doi = {10.3390/cells10030683},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {3},

pages = {1-16},

publisher = {MDPI},

abstract = {Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, 3 and 4. Genomic and methylomic variation differentiated the collection into two subpopulations designated as coastal and central (respectively from regions 1a; 1c and the other from 2; 3 and 4) which were linked to environmental variables such as relative precipitation. Here, we assessed how far genomic variation would be reflected in the metabolomes and if this could be linked to an adaptive trait. Metabolites were extracted from eight-week-old seedlings from each accession and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Princi-pal Component Analysis (PCA) of the derived metabolomes differentiated between samples from coastal and central subpopulations. The major sources of variation between seedling from the coastal and central subpopulations were identified. The central subpopulation was typified by significant increases in alanine, aspartate and glutamate metabolism and the tricarboxylic acid (TCA) cycle. Coastal subpopulation exhibited elevated levels of the auxin, indolacetic acid and rhamnose. The metabolomes of the seedling were also determined following the imposition of drought stress for seven days. The central subpopulation exhibited a metabolomic shift in response to drought, but no significant changes were seen in the coastal one. The drought responses in the central subpopu-lation were typified by changes in amino acids, increasing the glutamine that could be functioning as a stress signal. There were also changes in sugars that were likely to be an osmotic counter to drought, and changes in bioenergetic metabolism. These data indicate that genomic variation in our Turkish Brachypodium collection is largely reflected as distinctive metabolomes (“metabolotypes”) through which drought tolerance might be mediated. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85100110960,

title = {Defining the cell wall, cell cycle and chromatin landmarks in the responses of brachypodium distachyon to salinity},

author = { E.A. Wolny and A. Skalska and A.J. Brąszewska-Zalewska and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100110960&doi=10.3390%2fijms22020949&partnerID=40&md5=aacee36bf01649a69d0bc62ec3e40d65},

doi = {10.3390/ijms22020949},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {2},

pages = {1-23},

publisher = {MDPI AG},

abstract = {Excess salinity is a major stress that limits crop yields. Here, we used the model grass Brachypodium distachyon (Brachypodium) reference line Bd21 in order to define the key molecular events in the responses to salt during germination. Salt was applied either throughout the germination period (“salt stress”) or only after root emergence (“salt shock”). Germination was affected at ≥100 mM and root elongation at ≥75 mM NaCl. The expression of arabinogalactan proteins (AGPs), FLA1, FLA10, FLA11, AGP20 and AGP26, which regulate cell wall expansion (especially FLA11), were mostly induced by the “salt stress” but to a lesser extent by “salt shock”. Cytological assessment using two AGP epitopes, JIM8 and JIM13 indicated that “salt stress” increases the fluorescence signals in rhizodermal and exodermal cell wall. Cell division was suppressed at >75 mM NaCl. The cell cycle genes (CDKB1; CDKB2; CYCA3; CYCB1; WEE1) were induced by “salt stress” in a concentration-dependent manner but not CDKA, CYCA and CYCLIN-D4-1-RELATED. Under “salt shock”, the cell cycle genes were optimally expressed at 100 mM NaCl. These changes were consistent with the cell cycle arrest, possibly at the G1 phase. The salt-induced genomic damage was linked with the oxidative events via an increased glutathione accumulation. Histone acetylation and methylation and DNA methylation were visualized by immunofluorescence. Histone H4 acetylation at lysine 5 increased strongly whereas DNA methylation decreased with the application of salt. Taken together, we suggest that salt-induced oxidative stress causes genomic damage but that it also has epigenetic effects, which might modulate the cell cycle and AGP expression gene. Based on these landmarks, we aim to encourage functional genomics studies on the responses of Brachypodium to salt. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85105054260,

title = {Allotetraploidization in brachypodium may have led to the dominance of one parent’s metabolome in germinating seeds},

author = { A. Skalska and E.A. Wolny and M. Beckmann and J.H. Doonan and R. Hasterok and L.A.J. Mur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85105054260&doi=10.3390%2fcells10040828&partnerID=40&md5=f2b582d61460aff5dc06392d44d8357d},

doi = {10.3390/cells10040828},

issn = {20734409},

year  = {2021},

date = {2021-01-01},

journal = {Cells},

volume = {10},

number = {4},

publisher = {MDPI},

abstract = {Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85088698921,

title = {Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors},

author = { S.P. Gordon and B. Contreras-Moreira and J.J. Levy and A. Djamei and A. Czedik-Eysenberg and V.S. Tartaglio and A. Session and J. Martin and A. Cartwright and A. Katz and V.R. Singan and E. Goltsman and K. Barry and V.H. Dinh-Thi and B. Chalhoub and A. Díaz-Pérez and R. Sancho and J. Lusinska and E.A. Wolny and C. Nibau and J.H. Doonan and L.A.J. Mur and C. Plott and J. Jenkins and S.P. Hazen and S.J. Lee and S. Shu and D. Goodstein and D. Rokhsar and J. Schmutz and R. Hasterok and P. Catalán and J.P. Vogel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088698921&doi=10.1038%2fs41467-020-17302-5&partnerID=40&md5=a244ebf9c21dbfb16be4ae4a1e58bd83},

doi = {10.1038/s41467-020-17302-5},

issn = {20411723},

year  = {2020},

date = {2020-01-01},

journal = {Nature Communications},

volume = {11},

number = {1},

publisher = {Nature Research},

abstract = {Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution. © 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.},

note = {27},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85090784148,

title = {Genetic and methylome variation in Turkish brachypodium distachyon accessions differentiate two geographically distinct subpopulations},

author = { A. Skalska and C. Stritt and M. Wyler and H.W. Williams and M. Vickers and J. Han and M. Tuna and G.S. Tuna and K. Susek and M. Swain and R.K. Wóycicki and S. Chaudhary and F. Corke and J.H. Doonan and A.C. Roulin and R. Hasterok and L.A.J. Mur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090784148&doi=10.3390%2fijms21186700&partnerID=40&md5=e48f545ce9d2c4d90b4f6d5b9a8099fa},

doi = {10.3390/ijms21186700},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-17},

publisher = {MDPI AG},

abstract = {Brachypodium distachyon (Brachypodium) is a non-domesticated model grass species that can be used to test if variation in genetic sequence or methylation are linked to environmental differences. To assess this, we collected seeds from 12 sites within five climatically distinct regions of Turkey. Seeds from each region were grown under standardized growth conditions in the UK to preserve methylated sequence variation. At six weeks following germination, leaves were sampled and assessed for genomic and DNA methylation variation. In a follow-up experiment, phenomic approaches were used to describe plant growth and drought responses. Genome sequencing and population structure analysis suggested three ancestral clusters across the Mediterranean, two of which were geographically separated in Turkey into coastal and central subpopulations. Phenotypic analyses showed that the coastal subpopulation tended to exhibit relatively delayed flowering and the central, increased drought tolerance as indicated by reduced yellowing. Genome-wide methylation analyses in GpC, CHG and CHH contexts also showed variation which aligned with the separation into coastal and central subpopulations. The climate niche modelling of both subpopulations showed a significant influence from the “Precipitation in the Driest Quarter” on the central subpopulation and “Temperature of the Coldest Month” on the coastal subpopulation. Our work demonstrates genetic diversity and variation in DNA methylation in Turkish accessions of Brachypodium that may be associated with climate variables and the molecular basis of which will feature in ongoing analyses. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85078255398,

title = {Progressive refinement of the karyotyping of Brachypodium genomes},

author = { R. Hasterok and K. Wang and G. Jenkins},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078255398&doi=10.1111%2fnph.16342&partnerID=40&md5=84a5a5dcbf3e23079c3ac64759477744},

doi = {10.1111/nph.16342},

issn = {0028646X},

year  = {2020},

date = {2020-01-01},

journal = {New Phytologist},

volume = {227},

number = {6},

pages = {1668-1675},

publisher = {Blackwell Publishing Ltd},

abstract = {Brachypodium distachyon is a weedy grass species that is firmly established as a model for the comparative and functional genomics of temperate cereals and grasses. Its simple, nuclear genome of five chromosomes contrasts it with other relatives of the genus with different, and usually higher, basic chromosome numbers and ploidy levels. This variation in karyotypic structure affords the possibility of reconstructing evolutionary pathways that have shaped the genome structure of extant species. This Tansley insight documents how key refinements in molecular cytogenetic approaches, from simple fluorescence in situ hybridization to comparative chromosome barcoding, have enabled genome structure studies and yielded valuable information about the drivers of karyotypic reorganization and evolution in the model grass genus Brachypodium. © 2019 The Authors New Phytologist © 2019 New Phytologist Trust},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85087457230,

title = {The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum},

author = { N. Borowska-Zuchowska and A. Kovaík and E. Robaszkiewicz and M. Tuna and G.S. Tuna and S.P. Gordon and J.P. Vogel and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087457230&doi=10.1111%2ftpj.14869&partnerID=40&md5=c5294c713fd03718dcd6e5695901a5c2},

doi = {10.1111/tpj.14869},

issn = {09607412},

year  = {2020},

date = {2020-01-01},

journal = {Plant Journal},

volume = {103},

number = {5},

pages = {1810-1825},

publisher = {Blackwell Publishing Ltd},

abstract = {Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage. © 2020 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85087866006,

title = {Comparative genomics of stenotrophomonas maltophilia and stenotrophomonas rhizophila revealed characteristic features of both species},

author = { A. Piński and J. Żur and R. Hasterok and K.T. Hupert-Kocurek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087866006&doi=10.3390%2fijms21144922&partnerID=40&md5=d3558a7364b4d6e0f87930ba3345b45d},

doi = {10.3390/ijms21144922},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {14},

pages = {1-20},

publisher = {MDPI AG},

abstract = {Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g.; chitin-binding protein; mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g.; glucosylglycerol-phosphate synthase; cold shock protein with the DUF1294 domain; and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85086465275,

title = {From single cell to plants: Mesophyll protoplasts as a versatile system for investigating plant cell reprogramming},

author = { T. Pasternak and K. Lystvan and A. Betekhtin and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086465275&doi=10.3390%2fijms21124195&partnerID=40&md5=0b8504d08f47ad16842619f402944d4f},

doi = {10.3390/ijms21124195},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {12},

pages = {1-15},

publisher = {MDPI AG},

abstract = {Plants are sessile organisms that have a remarkable developmental plasticity, which ensures their optimal adaptation to environmental stresses. Plant cell totipotency is an extreme example of such plasticity, whereby somatic cells have the potential to form plants via direct shoot organogenesis or somatic embryogenesis in response to various exogenous and/or endogenous signals. Protoplasts provide one of the most suitable systems for investigating molecular mechanisms of totipotency, because they are effectively single cell populations. In this review, we consider the current state of knowledge of the mechanisms that induce cell proliferation from individual, differentiated somatic plant cells. We highlight initial explant metabolic status, ploidy level and isolation procedure as determinants of successful cell reprogramming. We also discuss the importance of auxin signalling and its interaction with stress-regulated pathways in governing cell cycle induction and further stages of plant cell totipotency. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85085871596,

title = {A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum},

author = { K. Hus and A. Betekhtin and A. Piński and M. Rojek-Jelonek and E. Grzebelus and C. Nibau and M. Gao and K.E. Jaeger and G. Jenkins and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085871596&doi=10.3389%2ffpls.2020.00614&partnerID=40&md5=b86deda01a9059410a6d9ffe28faed8e},

doi = {10.3389/fpls.2020.00614},

issn = {1664462X},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in Plant Science},

volume = {11},

publisher = {Frontiers Media S.A.},

abstract = {The CRISPR/Cas9 system enables precise genome editing and is a useful tool for functional genomic studies. Here we report a detailed protocol for targeted genome editing in the model grass Brachypodium distachyon and its allotetraploid relative B. hybridum, describing gRNA design, a transient protoplast assay to test gRNA efficiency, Agrobacterium-mediated transformation and the selection and analysis of regenerated plants. In B. distachyon, we targeted the gene encoding phytoene desaturase (PDS), which is a crucial enzyme in the chlorophyll biosynthesis pathway. The albino phenotype of mutants obtained confirmed the effectiveness of the protocol for functional gene analysis. Additionally, we targeted two genes related to cell wall maintenance, encoding a fasciclin-like arabinogalactan protein (FLA) and a pectin methylesterase (PME), also in B. distachyon. Two genes encoding cyclin-dependent kinases (CDKG1 and CDKG2), which may be involved in DNA recombination were targeted in both B. distachyon and B. hybridum. Cas9 activity induces mainly insertions or deletions, resulting in frameshift mutations that, may lead to premature stop codons. Because of the close phylogenetic relationship between Brachypodium species and key temperate cereals and forage grasses, this protocol should be easily adapted to target genes underpinning agronomically important traits. © Copyright © 2020 Hus, Betekhtin, Pinski, Rojek-Jelonek, Grzebelus, Nibau, Gao, Jaeger, Jenkins, Doonan and Hasterok.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079083785,

title = {In vitro tissue culture in brachypodium: Applications and challenges},

author = { A. Betekhtin and K. Hus and M. Rojek-Jelonek and E.U. Kurczyńska and C. Nibau and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079083785&doi=10.3390%2fijms21031037&partnerID=40&md5=f5b279c30079e29e77cf4ca674cd3454},

doi = {10.3390/ijms21031037},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {3},

publisher = {MDPI AG},

abstract = {Brachypodium distachyon has become an excellent model for plant breeding and bioenergy grasses that permits many fundamental questions in grass biology to be addressed. One of the constraints to performing research in many grasses has been the difficulty with which they can be genetically transformed and the generally low frequency of such transformations. In this review, we discuss the contribution that transformation techniques have made in Brachypodium biology as well as how Brachypodium could be used to determine the factors that might contribute to transformation efficiency. In particular, we highlight the latest research on the mechanisms that govern the gradual loss of embryogenic potential in a tissue culture and propose using B. distachyon as a model for other recalcitrant monocots. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85074666863,

title = {Comparatively barcoded chromosomes of brachypodium perennials tell the story of their karyotype structure and evolution},

author = { J. Lusinska and A. Betekhtin and D. López-Alvarez and P. Catalán and G. Jenkins and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074666863&doi=10.3390%2fijms20225557&partnerID=40&md5=1e87ac6eba426f4ef1f180cb67cf71f1},

doi = {10.3390/ijms20225557},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {22},

publisher = {MDPI AG},

abstract = {The Brachypodium genus is an informative model system for studying grass karyotype organization. Previous studies of a limited number of species and reference chromosomes have not provided a comprehensive picture of the enigmatic phylogenetic relationships in the genus. Comparative chromosome barcoding, which enables the reconstruction of the evolutionary history of individual chromosomes and their segments, allowed us to infer the relationships between putative ancestral karyotypes of extinct species and extant karyotypes of current species. We used over 80 chromosome-specific BAC (bacterial artificial chromosome) clones derived from five reference chromosomes of B. distachyon as probes against the karyotypes of twelve accessions representing five diploid and polyploid Brachypodium perennials. The results showed that descending dysploidy is common in Brachypodium and occurs primarily via nested chromosome fusions. Brachypodium distachyon was rejected as a putative ancestor for allotetraploid perennials and B. stacei for B. mexicanum. We propose two alternative models of perennial polyploid evolution involving either the incorporation of a putative x = 5 ancestral karyotype with different descending dysploidy patterns compared to B. distachyon chromosomes or hybridization of two x = 9 ancestors followed by genome doubling and descending dysploidy. Details of the karyotype structure and evolution in several Brachypodium perennials are revealed for the first time. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85068449940,

title = {Detecting Brachypodium distachyon chromosomes Bd4 and Bd5 in MH- and X-ray-induced micronuclei using mcFISH},

author = { A. Kus and J. Szymanowska-Pułka and J. Kwaśniewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068449940&doi=10.3390%2fijms20112848&partnerID=40&md5=f40aef05841fe8d4b6057ef3081cefac},

doi = {10.3390/ijms20112848},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {11},

publisher = {MDPI AG},

abstract = {Micronuclei are biomarkers of genotoxic effects and chromosomal instability. They are formed when chromosome fragments or whole chromosomes fail to disjoin into daughter nuclei. We present qualitative and quantitative analyses of the involvement of specific chromosome regions of chromosomes Bd4 and Bd5 in the formation of micronuclei of Brachypodium distachyon root tip cells following maleic hydrazide (MH) treatment and X-radiation. This is visualised by cytomolecular approaches using bacterial artificial chromosome (BAC)-based multicolour fluorescence in situ hybridisation (mcFISH) in combination with 5S and 25S rDNA probes. The results showed that the long arm of submetacentric chromosome Bd4 forms micronuclei at twice the frequency of its short arm, suggesting that the former is more prone to double-strand breaks (DSBs). In contrast, no difference was observed in the frequency of micronuclei derived from the long and short arms of submetacentric chromosome Bd5. Interestingly, the proximal region of the short arm of Bd5 is more prone to DSBs than its distal part. This demonstrates that 5S rDNA and 35S rDNA loci are not “hot spots” for DNA breaks after the application of these mutagens. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85061604241,

title = {Stability and instability processes in the calli of Fagopyrum tataricum that have different morphogenic potentials},

author = { A. Betekhtin and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061604241&doi=10.1007%2fs11240-019-01575-w&partnerID=40&md5=645591d8a95ce3e965e098b879213554},

doi = {10.1007/s11240-019-01575-w},

issn = {01676857},

year  = {2019},

date = {2019-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {137},

number = {2},

pages = {343-357},

publisher = {Springer Netherlands},

abstract = {The morphogenic callus (MC) of Fagopyrum tataricum contains a large amount of flavonoids, especially rutin, and exhibits a high level of antioxidant activity. A non-morphogenic callus (NC) may appear on the surface of the MC after two to three years of cultivation and is then subjected to a consistently high level of oxidative stress. The elucidation of the molecular background of this instability is essential for gaining a better understanding of the somaclonal variation mechanisms in tissue cultures that have different morphogenic potentials. Thus, in this study we show that continuous oxidative stress in a NC might be connected with a rapid senescence process and as a result, in the upregulation of the genes that are connected with the telomere complexity, ethylene biosynthesis and the expression of DNA methyltransferases. Moreover, we analysed the presence of the hydroxyproline-rich glycoproteins in the calli and demonstrated the differences between the MC and NC. The LM2 antibody can be useful as a marker of the cells in the MC that are embryogenically determined, while the MAC207 antibody seems to be a positive marker of a MC as its signal was absent in the NC. This study also provides the first report on the effect of trichostatin A on the DNA methyltransferases and demethylases in a MC. © 2019, The Author(s).},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85066960172,

title = {Hydroxyproline-rich glycoproteins as markers of temperature stress in the leaves of brachypodium distachyon},

author = { A. Piński and A. Betekhtin and K. Sala and K. Godel-Jędrychowska and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066960172&doi=10.3390%2fijms20102571&partnerID=40&md5=83367841b3aa36bbcbe19816364135ad},

doi = {10.3390/ijms20102571},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {10},

publisher = {MDPI AG},

abstract = {Plants frequently encounter diverse abiotic stresses, one of which is environmental thermal stress. To cope with these stresses, plants have developed a range of mechanisms, including altering the cell wall architecture, which is facilitated by the arabinogalactan proteins (AGP) and extensins (EXT). In order to characterise the localisation of the epitopes of the AGP and EXT, which are induced by the stress connected with a low (4◦ C) or a high (40◦ C) temperature, in the leaves of Brachypodium distachyon, we performed immunohistochemical analyses using the antibodies that bind to selected AGP (JIM8; JIM13; JIM16; LM2 and MAC207), pectin/AGP (LM6) as well as EXT (JIM11; JIM12 and JIM20). The analyses of the epitopes of the AGP indicated their presence in the phloem and in the inner bundle sheath (JIM8; JIM13; JIM16 and LM2). The JIM16 epitope was less abundant in the leaves from the low or high temperature compared to the control leaves. The LM2 epitope was more abundant in the leaves that had been subjected to the high temperatures. In the case of JIM13 and MAC207, no changes were observed at the different temperatures. The epitopes of the EXT were primarily observed in the mesophyll and xylem cells of the major vascular bundle (JIM11; JIM12 and JIM20) and no correlation was observed between the presence of the epitopes and the temperature stress. We also analysed changes in the level of transcript accumulation of some of the genes encoding EXT, EXT-like receptor kinases and AGP in the response to the temperature stress. In both cases, although we observed the upregulation of the genes encoding AGP in stressed plants, the changes were more pronounced at the high temperature. Similar changes were observed in the expression profiles of the EXT and EXT-like receptor kinase genes. Our findings may be relevant for genetic engineering of plants with increased resistance to the temperature stress. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85065116283,

title = {Defining the genetic basis of plant–endophytic bacteria interactions},

author = { A. Piński and A. Betekhtin and K.T. Hupert-Kocurek and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85065116283&doi=10.3390%2fijms20081947&partnerID=40&md5=96b5990897aec8304bac8977b991dff7},

doi = {10.3390/ijms20081947},

issn = {16616596},

year  = {2019},

date = {2019-01-01},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

publisher = {MDPI AG},

abstract = {Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85067062279,

title = {Impact of chromosomal rearrangements on the interpretation of lupin karyotype evolution},

author = { K. Susek and W.K. Bielski and K.B. Czyż and R. Hasterok and S.A. Jackson and B. Wolko and B. Naganowska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067062279&doi=10.3390%2fgenes10040259&partnerID=40&md5=0c17558bb1b5a00a8c04502c058f521b},

doi = {10.3390/genes10040259},

issn = {20734425},

year  = {2019},

date = {2019-01-01},

journal = {Genes},

volume = {10},

number = {4},

publisher = {MDPI AG},

abstract = {Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32-52), but also for the basic chromosome number (x = 5-9; 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85061128284,

title = {Ribosomal DNA loci derived from Brachypodium stacei are switched off for major parts of the life cycle of Brachypodium hybridum},

author = { N. Borowska-Zuchowska and E. Robaszkiewicz and E.A. Wolny and A. Betekhtin and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061128284&doi=10.1093%2fjxb%2fery425&partnerID=40&md5=a123ef59aae852b182e62c863f89ff7c},

doi = {10.1093/jxb/ery425},

issn = {00220957},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Experimental Botany},

volume = {70},

number = {3},

pages = {871-883},

publisher = {Oxford University Press},

abstract = {Nucleolar dominance is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus while the rDNA loci derived from the other progenitor are transcriptionally silenced. There is substantial evidence that nucleolar dominance is regulated developmentally. This study focuses upon the establishment and/or maintenance of nucleolar dominance during different stages of development in the model grass allotetraploid Brachypodium hybridum. Fluorescence in situ hybridization with a 25S rDNA probe to cells in three-dimensional cytogenetic preparations showed that nucleolar dominance is present not only in root meristematic and differentiated cells of this species, but also in male meiocytes at prophase I, tetrads of microspores, and different embryonic tissues. The inactive state of Brachypodium stacei-originated rDNA loci was confirmed by silver staining. Only B. distachyon-derived 35S rDNA loci formed nucleoli in the aforementioned tissues, whereas B. stacei-like loci remained highly condensed and thus transcriptionally suppressed. The establishment of nucleolar dominance during earlier stages of B. hybridum embryo development cannot be ruled out. However, we propose that gradual pseudogenization of B. stacei-like loci in the evolution of the allotetraploid seems to be more likely. © 2018 The Author(s).},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85059798719,

title = {Dissecting the chromosomal composition of mutagen-induced micronuclei in Brachypodium distachyon using multicolour FISH},

author = { A. Kus and J. Kwaśniewska and J. Szymanowska-Pułka and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85059798719&doi=10.1093%2faob%2fmcy115&partnerID=40&md5=b9a66d550306425b0c916d43ec01570f},

doi = {10.1093/aob/mcy115},

issn = {03057364},

year  = {2018},

date = {2018-01-01},

journal = {Annals of Botany},

volume = {122},

number = {7},

pages = {1161-1171},

publisher = {Oxford University Press},

abstract = {Background and Aims Brachypodium distachyon (Brachypodium) is a model species for temperate cereals and other economically important grasses. Its favourable cytogenetic features and advanced molecular infrastructure make it a good model for understanding the mechanisms of instability of plant genomes after mutagenic treatment. The aim of this study was to qualitatively and quantitatively assess the composition and origin of micronuclei arising from genomic fracture, and to detect possible 'hot spots' for mutagen-induced DNA breaks. • Methods Seeds of Brachypodium were treated with maleic hydrazide (MH) or X-rays. The structure of mutagen-induced micronuclei was analysed in root-tip meristematic cells using multicolour fluorescence in situ hybridization (mcFISH) with various repetitive (5S rDNA; 25S rDNA; telomeric; centromeric) and low-repeat [small and large pools of bacterial artificial chromosome (BAC) clones specific for chromosome Bd1] DNA sequences. • Key Results The majority of micronuclei derive from large, acentric fragments. X-rays caused more interstitial DNA breaks than MH. Double-strand breaks rarely occurred in distal chromosome regions. Bd1 contributed to the formation of more mutagen-induced micronuclei than expected from random chromosome involvement. • Conclusions mcFISH with chromosome-specific BAC clones offers insight into micronuclei composition, in so far as it allows their origin and formation to be determined more specifically. A reliable assay for micronuclei composition is crucial for the development of modern genotoxicity tests using plant cells. The combination of mutagenic treatments and well-developed cytomolecular resources in Brachypodium make this model species very promising for plant mutagenesis research. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85057991726,

title = {Cell wall epitopes and endoploidy as reporters of embryogenic potential in brachypodium distachyon callus culture},

author = { A. Betekhtin and M. Rojek-Jelonek and K. Nowak and A. Piński and A. Milewska-Hendel and E.U. Kurczyńska and J.H. Doonan and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057991726&doi=10.3390%2fijms19123811&partnerID=40&md5=a019f7df04ed76fd5a1440b62abca7ae},

doi = {10.3390/ijms19123811},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {12},

publisher = {MDPI AG},

abstract = {Effective regeneration of callus tissue into embryos and then into whole plants is essential for plant biotechnology. The embryonic potential is often low and can further decrease with time in culture, which limits the utilisation of calli for transformation procedures and in vitro propagation. In this study, we show that the loss of embryogenic potential in callus cultures of Brachypodium distachyon is progressive over time. Flow cytometry analyses indicated endoploidy levels increased in 60-and 90-day-old calli with effective loss of the 2C DNA content peak in the latter. Analysis of indolic compounds content revealed a decrease in 60-and 90-day-old calli compared to either freshly isolated explants or 30-day-old calli. Immunohistochemical analysis revealed a decrease in arabinogalactan proteins (AGP) signal with the time of culture, but extensin (EXT) epitopes either increased (JIM12 epitopes) or decreased (JIM11 epitopes). The transcript accumulation levels of AGPs and EXTs confirmed these results, with most of AGP and EXT transcripts gradually decreasing. Some chimeric EXT transcripts significantly increased on the 30th day of culture, perhaps because of an increased embryogenic potential. Selected somatic embryogenesis-related genes and cyclins demonstrated a gradual decrease of transcript accumulation for YUCCA (YUC), AINTEGUMENTA-LIKE (AIL), BABY BOOM (BBM), and CLAVATA (CLV3) genes, as well as for most of the cyclins, starting from the 30th day of culture. Notably, WUSCHEL (WUS) transcript was detectable only on the 30th and 60th day and was not detectable in the zygotic embryos and in 90-day-old calli. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054137635,

title = {Germination and the early stages of seedling development in brachypodium distachyon},

author = { E.A. Wolny and A. Betekhtin and M. Rojek-Jelonek and A.J. Brąszewska-Zalewska and J. Lusinska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054137635&doi=10.3390%2fijms19102916&partnerID=40&md5=6bc3a0bce97cc709e1970b6a859568af},

doi = {10.3390/ijms19102916},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {10},

publisher = {MDPI AG},

abstract = {Successful germination and seedling development are crucial steps in the growth of a new plant. In this study, we investigated the course of the cell cycle during germination in relation to grain hydration in the model grass Brachypodium distachyon (Brachypodium) for the first time. Flow cytometry was performed to monitor the cell cycle progression during germination and to estimate DNA content in embryo tissues. The analyses of whole zygotic embryos revealed that the relative DNA content was 2C, 4C, 8C, and 16C. Endoreplicated nuclei were detected in the scutellum and coleorhiza cells, whereas the rest of the embryo tissues only had nuclei with a 2C and 4C DNA content. This study was accompanied by a spatiotemporal profile analysis of the DNA synthetic activity in the organs of Brachypodium embryos during germination using EdU labelling. Upon imbibition, nuclear DNA replication was initiated in the radicle within 11 h and subsequently spread towards the plumule. The first EdU-labelled prophases were observed after 14 h of imbibition. Analysis of selected genes that are involved in the regulation of the cell cycle, such as those encoding cyclin-dependent kinases and cyclins, demonstrated an increase in their expression profiles. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85043690137,

title = {FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa},

author = { A.J. Joachimiak and R. Hasterok and E. Sliwinska and K. Musiał and A. Grabowska-Joachimiak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043690137&doi=10.1007%2fs00709-018-1238-9&partnerID=40&md5=6d557cd07897efaa2df1b3fd9cc4b72d},

doi = {10.1007/s00709-018-1238-9},

issn = {0033183X},

year  = {2018},

date = {2018-01-01},

journal = {Protoplasma},

volume = {255},

number = {5},

pages = {1363-1372},

publisher = {Springer-Verlag Wien},

abstract = {The location of 5S and 35S rDNA sequences in chromosomes of four Aconitum subsp. Aconitum species was analyzed after fluorescence in situ hybridization (FISH). Both in diploids (2n = 2x = 16; Aconitum variegatum; A. degenii) and tetraploids (2n = 4× = 32; A. firmum; A. plicatum), rDNA repeats were localized exclusively on the shorter arms of chromosomes, in subterminal or pericentromeric sites. All analyzed species showed similar basal genome size (Cx = 5.31–5.71 pg). The most striking features of tetraploid karyotypes were the conservation of diploid rDNA loci and emergence of many additional 5S rDNA clusters. Chromosomal distribution of excessive ribosomal sites suggests their role in the secondary diploidization of tetraploid karyotypes. © 2018, The Author(s).},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054793804,

title = {Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum},

author = { J. Lusinska and J. Majka and A. Betekhtin and K. Susek and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054793804&doi=10.1093%2faob%2fmcy086&partnerID=40&md5=502a5a8f625a9f3465e1961f5b82860d},

doi = {10.1093/aob/mcy086},

issn = {03057364},

year  = {2018},

date = {2018-01-01},

journal = {Annals of Botany},

volume = {122},

number = {3},

pages = {445-459},

publisher = {Oxford University Press},

abstract = {Background and Aims The Brachypodium genus represents a useful model system to study grass genome organization. Palaeogenomic analyses (e.g. Murat F; Armero A; Pont C; Klopp C; Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics49: 490-496) have identified polyploidization and dysploidy as the prime mechanisms driving the diversity of plant karyotypes and nested chromosome fusions (NCFs) crucial for shaping grass chromosomes. This study compares the karyotype structure and evolution in B. distachyon (genome Bd), B. stacei (genome Bs) and in their putative allotetraploid B. hybridum (genomes BdBs). Methods Brachypodium chromosomes were measured and identified using multicolour fluorescence in situ hybridization (mcFISH). For higher resolution, comparative chromosome barcoding was developed using sets of low-repeat, physically mapped B. distachyon-derived bacterial artificial chromosome (BAC) clones. Key Results All species had rather small chromosomes, and essentially all in the Bs genome were morphometrically indistinguishable. Seven BACs combined with two rDNA-based probes provided unambiguous and reproducible chromosome discrimination. Comparative chromosome barcoding revealed NCFs that contributed to the reduction in the x = 12 chromosome number that has been suggested for the intermediate ancestral grass karyotype. Chromosome Bd3 derives from two NCFs of three ancestral chromosomes (Os2; Os8; Os10). Chromosome Bs6 shows an ancient Os8/Os10 NCF, whilst Bs4 represents Os2 only. Chromosome Bd4 originated from a descending dysploidy that involves two NCFs of Os12, Os9 and Os11. The specific distribution of BACs along Bs9 and Bs5, in both B. stacei and B. hybridum, suggests a Bs genome-specific Robertsonian rearrangement. Conclusions mcFISH-based karyotyping identifies all chromosomes in Brachypodium annuals. Comparative chromosome barcoding reveals rearrangements responsible for the diverse organization of Bd and Bs genomes and provides new data regarding karyotype evolution since the split of the two diploids. The fact that no chromosome rearrangements were observed in B. hybridum compared with the karyotypes of its phylogenetic ancestors suggests prolonged genome stasis after the formation of the allotetraploid. © 2018 The Author(s).},

note = {22},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85048889878,

title = {5-Azacitidine induces cell death in a tissue culture of brachypodium distachyon},

author = { A. Betekhtin and A. Milewska-Hendel and Ł. Chajec and M. Rojek-Jelonek and K. Nowak and J. Kwaśniewska and E.A. Wolny and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048889878&doi=10.3390%2fijms19061806&partnerID=40&md5=72a6b817774ef0346f00f6530b07a6ac},

doi = {10.3390/ijms19061806},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {6},

publisher = {MDPI AG},

abstract = {Morphological and histological observations revealed that, at a concentration of 50 µM, 5-azacitidine (5-azaC) totally inhibited the induction of embryogenic masses (EM), while the cultivation of explants (zygotic embryos; ZEs) in the presence of 5 µM of 5-azaC led to the formation of a callus with EM in 10% of the cases. Transmission electron microscopy (TEM) analyzes revealed the presence of the morphological and ultrastructural features that are typical for the vacuolar type of cell death in the callus cells that were treated. A TUNEL assay confirmed the presence of DNA double-strand breaks for the callus cells that had been treated with both 5 and 50 µM 5-azaC concentrations. Analysis of the gene expression of selected cell death markers demonstrated a reduced expression of metacaspase, protein executer 1 (EX1), and thioredoxin (TRX) in the callus cells that had been treated compared to the control culture. The strongest increase in the gene activity was characteristic for glutathione S-transferase (GST). Our studies also included an analysis of the distribution of some arabinogalactan proteins (AGPs) and extensin epitopes, which can be used as markers of cells that are undergoing death in a Brachypodium distachyon tissue culture. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85042854293,

title = {Organ and tissue-specific localisation of selected cell wall epitopes in the zygotic embryo of Brachypodium distachyon},

author = { A. Betekhtin and A. Milewska-Hendel and J. Lusinska and Ł. Chajec and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042854293&doi=10.3390%2fijms19030725&partnerID=40&md5=f697b77194807b245593766f2c341404},

doi = {10.3390/ijms19030725},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {3},

publisher = {MDPI AG},

abstract = {The plant cell wall shows a great diversity regarding its chemical composition, which may vary significantly even during different developmental stages. In this study, we analysed the distribution of several cell wall epitopes in embryos of Brachypodium distachyon (Brachypodium). We also described the variations in the nucleus shape and the number of nucleoli that occurred in some embryo cells. The use of transmission electron microscopy, and histological and immunolocalisation techniques permitted the distribution of selected arabinogalactan proteins, extensins, pectins, and hemicelluloses on the embryo surface, internal cell compartments, and in the context of the cell wall ultrastructure to be demonstrated. We revealed that the majority of arabinogalactan proteins and extensins were distributed on the cell surface and that pectins were the main component of the seed coat and other parts, such as the mesocotyl cell walls and the radicula. Hemicelluloses were localised in the cell wall and outside of the radicula protodermis, respectively. The specific arrangement of those components may indicate their significance during embryo development and seed germination, thus suggesting the importance of their protective functions. Despite the differences in the cell wall composition, we found that some of the antibodies can be used as markers to identify specific cells and the parts of the developing Brachypodium embryo. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85042554408,

title = {Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus},

author = { Y. Li and S. Zuo and Z. Zhang and Z. Li and J. Han and Z. Chu and R. Hasterok and K. Wang},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042554408&doi=10.1111%2ftpj.13832&partnerID=40&md5=9bbcdd0af237af6daca5b7bb261d68f0},

doi = {10.1111/tpj.13832},

issn = {09607412},

year  = {2018},

date = {2018-01-01},

journal = {Plant Journal},

volume = {93},

number = {6},

pages = {1088-1101},

publisher = {Blackwell Publishing Ltd},

abstract = {Brachypodium distachyon is a well-established model monocot plant, and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as Avena sativa (oats), Hordeum vulgare (barley) and Triticum aestivum (wheat). Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. As the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus. In this study, we isolated the centromeric DNA of the B. distachyon reference line Bd21 and characterized its composition via the chromatin immunoprecipitation of the nucleosomes that contain the centromere-specific histone CENH3. We revealed that the centromeres of Bd21 have the features of typical multicellular eukaryotic centromeres. Strikingly, these centromeres contain relatively few centromeric satellite DNAs; in particular, the centromere of chromosome 5 (Bd5) consists of only ~40 kb. Moreover, the centromeric retrotransposons in B. distachyon (CRBds) are evolutionarily young. These transposable elements are located both within and adjacent to the CENH3 binding domains, and have similar compositions. Moreover, based on the presence of CRBds in the centromeres, the species in this study can be grouped into two distinct lineages. This may provide new evidence regarding the phylogenetic relationships within the Brachypodium genus. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85058241904,

title = {Assessment of the molecular cytogenetic, morphometric and biochemical parameters of Deschampsia Antarctica from its southern range limit in maritime Antarctic},

author = { D. Navrotska and I. Andreev and A. Betekhtin and M. Rojek-Jelonek and I. Parnikoza and G. Myryuta and O. Poronnik and N. Miryuta and J. Szymanowska-Pułka and V. Grakhov and R. Ivannikov and R. Hasterok and V. Kunakh},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058241904&doi=10.24425%2f118759&partnerID=40&md5=4c9a8d4e1bb3c73145abf3503963325d},

doi = {10.24425/118759},

issn = {01380338},

year  = {2018},

date = {2018-01-01},

journal = {Polish Polar Research},

volume = {39},

number = {4},

pages = {525-548},

publisher = {Polish Academy of Sciences},

abstract = {Different chromosomal forms of Deschampsia antarctica Desv. (Poaceae), including diploids (2n=26), hypotriploid (2n=36-38) and a genotype with an occasional occurrence of B chromosome (2n=261B) that originated from southern marginal populations (Argentine Islands region; maritime Antarctic) were studied using molecular cytogenetic, morphometric and biochemical methods. FISH analysis revealed variations in the number of rDNA sites between the diploid and hypotriploid plants. The genome size varied among plants with a different chromosome number and was on average 10.88 pg/2C for diploids and 16.46 pg/2C for hypotriploid. The mean values of leaf length of plants grown in vitro varied within a range of 5.23-9.56 cm. The total phenolic content ranged from 51.10 to 105.40 mg/g, and the total flavonoid content ranged from 1.22 to 4.67 mg/g. The amount of phenolic compounds did not differ significantly between the genotypes, while a variation in the flavonoid content was observed for L59 and DAR12. The diploids did not differ significantly among each other in terms of the number of rDNA loci, but differed slightly in their genome size. The individuals of DAR12 carrying B chromosome were similar to other diploids in terms of their genome size, but statistically differed in leaf length. The hypotriploid had both a greater number of rDNA sites and a larger genome size. No statistical correlations were observed between the genome size and leaf length or genome size and accumulation of phenolic and flavonoid compounds. The results of this study suggest that D. antarctica plants from the southern edge of the range are characterised by the heterogeneity of the studied parameters. © 2018 Walter de Gruyter GmbH.All right reserved.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85023774270,

title = {Epigenetics of the preferential silencing of Brachypodium stacei-originated 35S rDNA loci in the allotetraploid grass Brachypodium hybridum},

author = { N. Borowska-Zuchowska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85023774270&doi=10.1038%2fs41598-017-05413-x&partnerID=40&md5=b5e39720ac65854b7840ca395d7bb6b5},

doi = {10.1038/s41598-017-05413-x},

issn = {20452322},

year  = {2017},

date = {2017-01-01},

journal = {Scientific Reports},

volume = {7},

number = {1},

publisher = {Nature Publishing Group},

abstract = {Nucleolar dominance (ND), initially described as 'differential amphiplasty', is a phenomenon observed in some plant and animal allopolyploids and hybrids in which the selective suppression of the activity of 35S rRNA gene loci that have been inherited from one of the two or more ancestral genomes occurs. Although more than 80 years have passed since the discovery of ND, there is still a significant lack in our understanding of the mechanisms that determine this phenomenon. Here, we aimed to investigate the epigenetic status of 35S rRNA gene loci in the monocotyledonous Brachypodium hybridum, which is an allotetraploid that has resulted from a cross between B. distachyon and B. stacei. We revealed that the repressed B. stacei-inherited rDNA loci are characterised by a high level of DNA methylation. The global hypomethylation of B. hybridum nuclear DNA induced by 5-azacytidine, however, seems to be insufficient for the transcriptional reactivation of these loci, which indicates that factors other than DNA methylation are behind the suppression of B. stacei-originated loci. We also showed that the transcriptionally active and silenced fractions of rRNA genes that had been inherited from B. distachyon occupy different domains within the chromocentres adjacent to the nucleolus, depending on their epigenetic status. © 2017 The Author(s).},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85013775595,

title = {Histone H3 and H4 acetylation patterns are more dynamic than those of DNA methylation in Brachypodium distachyon embryos during seed maturation and germination},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and D. Kroczek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85013775595&doi=10.1007%2fs00709-017-1088-x&partnerID=40&md5=8beaeb9cef0bb0cad966271c94b002e0},

doi = {10.1007/s00709-017-1088-x},

issn = {0033183X},

year  = {2017},

date = {2017-01-01},

journal = {Protoplasma},

volume = {254},

number = {5},

pages = {2045-2052},

publisher = {Springer-Verlag Wien},

abstract = {The transition of seeds from a dry to a metabolically active state requires significant changes in both the spatial and temporal patterns of gene expression, and this transcriptional reprogramming involves various modifications of the chromatin structure. There are several factors that can greatly influence the structure of chromatin, one of which is the chemical modifications of histone proteins and DNA itself. In this study, we analysed the distribution of three epigenetic markers, i.e. acetylation of histone H4 (H4K16ac) and histone H3 (H3K18ac) as well as DNA methylation (5mC) in Brachypodium distachyon embryos during the four stages of seed development—maturation, desiccation (quiescence), imbibition and germination. Our results indicate that both H4K16ac and H3K18ac are at a very high level in embryos during seed imbibition, but that the patterns of DNA methylation are considerably more stable in embryos during seed development. © 2017, The Author(s).},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021211772,

title = {Epigenomic diversification within the genus Lupinus},

author = { K. Susek and A.J. Brąszewska-Zalewska and A.J. Bewick and R. Hasterok and R.J. Schmitz and B. Naganowska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021211772&doi=10.1371%2fjournal.pone.0179821&partnerID=40&md5=d1e72da8b641004db9c57e2d2f85606f},

doi = {10.1371/journal.pone.0179821},

issn = {19326203},

year  = {2017},

date = {2017-01-01},

journal = {PLoS ONE},

volume = {12},

number = {6},

publisher = {Public Library of Science},

abstract = {Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order to gain a better understanding of the epigenetic organisation of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n = 40), L. albus (2n = 50) and L. luteus (2n = 52), and the legume model plant Medicago truncatula (2n = 16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG; CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n = 32), L. digitatus (2n = 36), L. micranthus (2n = 52) and L. pilosus (2n = 42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome. © 2017 Susek et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85014957702,

title = {Nuclear genome stability in long-term cultivated callus lines of Fagopyrum tataricum (L.) Gaertn},

author = { A. Betekhtin and M. Rojek-Jelonek and J. Jaskowiak and A. Milewska-Hendel and J. Kwaśniewska and Y. Kostyukova and E.U. Kurczyńska and N. Rumyantseva and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85014957702&doi=10.1371%2fjournal.pone.0173537&partnerID=40&md5=8a4e7fc7b0fee91c193c03db23eaecb2},

doi = {10.1371/journal.pone.0173537},

issn = {19326203},

year  = {2017},

date = {2017-01-01},

journal = {PLoS ONE},

volume = {12},

number = {3},

publisher = {Public Library of Science},

abstract = {Long-term cultivated Fagopyrum tataricum (L.) Gaertn. (Tartary buckwheat) morphogenic and non-morphogenic callus lines are interesting systems for gaining a better understanding of the mechanisms that are responsible for the genetic stability and instability of a plant tissue culture. In this work, we used histological sections and transmission electron microscopy to identify and describe the morphology of the nuclei of all of the analysed callus lines. We demonstrated that the embryogenic callus cells had prominent round nuclei that did not contain heterochromatin clumps in contrast to the non-morphogenic callus lines, in which we found nuclei that had multiple lobes. Flow cytometry analysis revealed significant differences in the relative DNA content between the analysed calli. All of the analysed morphogenic callus lines had peaks from 2C to 8C as compared to the nonmorphogenic callus lines, whose peaks did not reflect any regular DNA content and exceeded 8C and 16C for the line 6p1 and 16C and 32C for the callus line 10p2A. The results showed that non-morphogenic calli are of an aneuploid nature. The TUNEL test enabled us to visualise the nuclei that had DNA fragmentation in both the morphogenic and non-morphogenic lines. We revealed significantly higher frequencies of positively labelled nuclei in the non-morphogenic lines than in the morphogenic lines. In the case of the morphogenic lines, the highest observed frequency of TUNEL-positive nuclei was 7.7% for lines 2-3. In the non-morphogenic calli, the highest level of DNA damage (68.5%) was revealed in line 6p1. These results clearly indicate greater genome stability in the morphogenic lines. © 2017 Betekhtin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85010782761,

title = {Brachypodium distachyon - A useful model in the qualification of mutagen-induced micronuclei using multicolor FISH},

author = { A. Kus and J. Kwaśniewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010782761&doi=10.1371%2fjournal.pone.0170618&partnerID=40&md5=7fa1a05186c4880941f6e328facb4bec},

doi = {10.1371/journal.pone.0170618},

issn = {19326203},

year  = {2017},

date = {2017-01-01},

journal = {PLoS ONE},

volume = {12},

number = {1},

publisher = {Public Library of Science},

abstract = {Brachypodium distachyon (Brachypodium) is now intensively utilized as a model grass species in various biological studies. Its favorable cytological features create a unique foundation for a convenient system in mutagenesis, thereby potentially enabling the 'hot spots' and 'cold spots' of DNA damage in its genome to be analyzed. The aim of this study was to analyze the involvement of 5S rDNA, 25S rDNA, the Arabidopsis-type (TTTAGGG)n telomeric sequence and the Brachypodium-originated centromeric BAC clone CB33J12 in the micronuclei formation in Brachypodium root tip cells that were subjected to the chemical clastogenic agent maleic hydrazide (MH). To the best of our knowledge, this is the first use of a multicolor fluorescence in situ hybridization (mFISH) with four different DNA probes being used simultaneously to study plant mutagenesis. A quantitative analysis allowed ten types of micronuclei, which were characterized by the presence or absence of specific FISH signal(s), to be distinguished, thus enabling some specific rules governing the composition of the MH-induced micronuclei with the majority of them originating from the terminal regions of chromosomes, to be identified. The application of rDNA sequences as probes showed that 5S rDNA-bearing chromosomes are involved in micronuclei formation more frequently than the 25S rDNA-bearing chromosomes. These findings demonstrate the promising potential of Brachypodium to be a useful model organism to analyze the effects of various genotoxic agents on the plant nuclear genome stability, especially when the complex FISHbased and chromosome-specific approaches such as chromosome barcoding and chromosome painting will be applied in future studies. © 2017 Kus et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85006076427,

title = {Recreating stable Brachypodium hybridum allotetraploids by uniting the divergent genomes of B. distachyon and B. stacei},

author = { V.H.D. Thi and O. Coriton and I. Le Clainche and D. Arnaud and S.P. Gordon and G. Linc and P. Catalán and R. Hasterok and J.P. Vogel and J. Jahier and B. Chalhoub},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85006076427&doi=10.1371%2fjournal.pone.0167171&partnerID=40&md5=e9205e0d2d01faa997ab8dbfa3d5d5e4},

doi = {10.1371/journal.pone.0167171},

issn = {19326203},

year  = {2016},

date = {2016-01-01},

journal = {PLoS ONE},

volume = {11},

number = {12},

publisher = {Public Library of Science},

abstract = {Brachypodium hybridum (2n = 30) is a natural allopolyploid with highly divergent subgenomes derived from two extant diploid species, B. distachyon (2n = 10) and B. stacei (2n = 20) that differ in chromosome evolution and number. We created synthetic B. hybridum allotetraploids by hybridizing various lines of B. distachyon and B. stacei. The initial amphihaploid F1 interspecific hybrids were obtained at low frequencies when B. distachyon was used as the maternal parent (0.15% or 0.245% depending on the line used) and were sterile. No hybrids were obtained from reciprocal crosses or when autotetraploids of the parental species were crossed. Colchicine treatment was used to double the genome of the F1 amphihaploid lines leading to allotetraploids. The genome-doubled F1 plants produced a few S1 (first selfed generation) seeds after self-pollination. S1 plants from one parental combination (Bd3-1×Bsta5) were fertile and gave rise to further generations whereas those of another parental combination (Bd21×ABR114) were sterile, illustrating the importance of the parental lineages crossed. The synthetic allotetraploids were stable and resembled the natural B. hybridum at the phenotypic, cytogenetic and genomic levels. The successful creation of synthetic B. hybridum offers the possibility to study changes in genome structure and regulation at the earliest stages of allopolyploid formation in comparison with the parental species and natural B. hybridum. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84997354235,

title = {Spatial distribution of selected chemical cell wall components in the embryogenic callus of brachypodium distachyon},

author = { A. Betekhtin and M. Rojek-Jelonek and A. Milewska-Hendel and R. Gawecki and J. Karcz and E.U. Kurczyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84997354235&doi=10.1371%2fjournal.pone.0167426&partnerID=40&md5=d5dadb0308d02b7c3e39490a13f7fd39},

doi = {10.1371/journal.pone.0167426},

issn = {19326203},

year  = {2016},

date = {2016-01-01},

journal = {PLoS ONE},

volume = {11},

number = {11},

publisher = {Public Library of Science},

abstract = {Brachypodium distachyon L. Beauv. (Brachypodium) is a species that has become an excellent model system for gaining a better understanding of various areas of grass biology and improving plant breeding. Although there are some studies of an in vitro Brachypodium culture including somatic embryogenesis, detailed knowledge of the composition of the main cell wall components in the embryogenic callus in this species is missing. Therefore, using the immunocytochemical approach, we targeted 17 different antigens of which five were against the arabinogalactan proteins (AGP), three were against extensins, six recognised pectic epitopes and two recognised hemicelluloses. These studies were complemented by histological and scanning electron microscopy (SEM) analyses. We revealed that the characteristic cell wall components of Brachypodium embryogenic calli are AGP epitopes that are recognised by the JIM16 and LM2 antibodies, an extensin epitope that is recognised by the JIM11 antibody and a pectic epitopes that is recognised by the LM6 antibody. Furthermore, we demonstrated that AGPs and pectins are the components of the extracellular matrix network in Brachypodium embryogenic culture. Additionally, SEM analysis demonstrated the presence of an extracellular matrix on the surface of the calli cells. In conclusion, the chemical compositions of the cell walls and ECMSN of Brachypodium callus show spatial differences that correlate with the embryogenic character of the cells. Thus, the distribution of pectins, AGPs and hemicelluloses can be used as molecular markers of embryogenic cells. The presented data extends the knowledge about the chemical composition of the embryogenic callus cells of Brachypodium. © 2016 Betekhtin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {21},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84991710968,

title = {Cytomolecular analysis of ribosomal DNA evolution in a natural allotetraploid brachypodium hybridum and its putative ancestors-dissecting complex repetitive structure of intergenic spacers},

author = { N. Borowska-Zuchowska and M. Kwaśniewski and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991710968&doi=10.3389%2ffpls.2016.01499&partnerID=40&md5=88f59b413c0074698edc2329523cb27d},

doi = {10.3389/fpls.2016.01499},

issn = {1664462X},

year  = {2016},

date = {2016-01-01},

journal = {Frontiers in Plant Science},

volume = {7},

number = {OCTOBER2016},

publisher = {Frontiers Media S.A.},

abstract = {Nucleolar dominance is an epigenetic phenomenon associated with nuclear 35S rRNA genes and consists in selective suppression of gene loci inherited from one of the progenitors in the allopolyploid. Our understanding of the exact mechanisms that determine this process is still fragmentary, especially in case of the grass species. This study aimed to shed some light on the molecular basis of this genome-specific inactivation of 35S rDNA loci in an allotetraploid Brachypodium hybridum (2n = 30), which arose from the interspecific hybridization between two diploid ancestors that were very similar to modern B. distachyon (2n = 10) and B. stacei (2n = 20). Using fluorescence in situ hybridization with 25S rDNA and chromosome-specific BAC clones as probes we revealed that the nucleolar dominance is present not only in meristematic root-tip cells but also in differentiated cell fraction of B. hybridum. Additionally, the intergenic spacers (IGSs) from both of the putative ancestors and the allotetraploid were sequenced and analyzed. The presumptive transcription initiation sites, spacer promoters and repeated elements were identified within the IGSs. Two different length variants, 2.3 and 3.5 kb, of IGSs were identified in B. distachyon and B. stacei, respectively, however only the IGS that had originated from B. distachyon-like ancestor was present in the allotetraploid. The amplification pattern of B. hybridum IGSs suggests that some genetic changes occurred in inactive B. stacei-like rDNA loci during the evolution of the allotetraploid. We hypothesize that their preferential silencing is an effect of structural changes in the sequence rather than just the result of the sole inactivation at the epigenetic level. © 2016 Borowska-Zuchowska, Kwasniewski and Hasterok.},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84991338062,

title = {The arrangement of Brachypodium distachyon chromosomes in interphase nuclei},

author = { E. Robaszkiewicz and D. Idziak-Helmcke and M.A. Tkacz and K. Chromiński and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991338062&doi=10.1093%2fjxb%2ferw325&partnerID=40&md5=8a7c33ee8380b9515384b6e89105fe0e},

doi = {10.1093/jxb/erw325},

issn = {00220957},

year  = {2016},

date = {2016-01-01},

journal = {Journal of Experimental Botany},

volume = {67},

number = {18},

pages = {5571-5583},

publisher = {Oxford University Press},

abstract = {The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84983349098,

title = {Chromosome territory modeller and viewer},

author = { M.A. Tkacz and K. Chromiński and D. Idziak-Helmcke and E. Robaszkiewicz and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983349098&doi=10.1371%2fjournal.pone.0160303&partnerID=40&md5=d9d45b53bba93bb786f6f478871c4ab4},

doi = {10.1371/journal.pone.0160303},

issn = {19326203},

year  = {2016},

date = {2016-01-01},

journal = {PLoS ONE},

volume = {11},

number = {8},

publisher = {Public Library of Science},

abstract = {This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi-a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass Brachypodium distachyon. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license. © 2016 Tkacz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84983408168,

title = {A first Glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping},

author = { K. Susek and W.K. Bielski and R. Hasterok and B. Naganowska and B. Wolko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983408168&doi=10.3389%2ffpls.2016.01152&partnerID=40&md5=77e59bb0e8caf134d2c0deaef5895d46},

doi = {10.3389/fpls.2016.01152},

issn = {1664462X},

year  = {2016},

date = {2016-01-01},

journal = {Frontiers in Plant Science},

volume = {7},

publisher = {Frontiers Media S.A.},

abstract = {Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins (OWL) demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n = 32-52), basic chromosome numbers (x = 5-7; 9; 13) and in nuclear genome size (2C DNA = 0.97-2.68 pg). Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution. In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all “single-locus” in L. angustifolius, in the wild lupins these clones proved to be “single-locus,” “single-locus” with additional signals, “repetitive” or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g., L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the relationships between the lupins and the extensive cytological diversity within this group. In this study we premise that lupin genomes underwent at least two rounds of fusion and fission events resulting in the reduction in chromosome number from 2n = 52 through 2n = 40 to 2n = 32, followed by chromosome number increment to 2n = 42. © 2016 Susek, Bielski, Hasterok, Naganowska and Wolko.},

note = {15},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84948394533,

title = {Spatial distribution of centromeres and telomeres at interphase varies among Brachypodium species},

author = { D. Idziak-Helmcke and E. Robaszkiewicz and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948394533&doi=10.1093%2fjxb%2ferv369&partnerID=40&md5=38522a8dc5997a545e3f46104ed35bbb},

doi = {10.1093/jxb/erv369},

issn = {00220957},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Experimental Botany},

volume = {66},

number = {21},

pages = {6623-6634},

publisher = {Oxford University Press},

abstract = {In this study the 3-D distribution of centromeres and telomeres was analysed in the interphase nuclei of three Brachypodium species, i.e. B. distachyon (2n=10), B. stacei (2n=20) and B. hybridum (2n=30), which is presumably a hybrid between the first two species. Using fluorescence in situ hybridization (FISH) with centromeric and telomeric DNA probes, it was observed that the majority of B. distachyon nuclei in the root tip cells displayed the Rabl configuration while both B. stacei and B. hybridum mostly lacked the centromere-telomere polarization. In addition, differentiated leaf cells of B. distachyon did not display the Rabl pattern. In order to analyse the possible connection between the occurrence of the Rabl pattern and the phase of cell cycle or DNA content, FISH was combined with digital image cytometry. The results revealed that the frequency of nuclei with the Rabl configuration in the root tip nuclei was positively correlated with an increase in DNA content, which resulted from DNA replication. Also, the analysis of the influence of the nuclear shape on the nuclear architecture indicated that an increasing elongation of the nuclei negatively affected the occurrence of the Rabl pattern. Some possible explanations of these phenomena are discussed. © 2015 The Author.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84944031628,

title = {In situ analysis of epigenetic modifications in the chromatin of Brachypodium distachyon embryos},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and D. Kroczek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84944031628&doi=10.1080%2f15592324.2015.1011948&partnerID=40&md5=3b979188a97b567a2cf78e22419d2247},

doi = {10.1080/15592324.2015.1011948},

issn = {15592316},

year  = {2015},

date = {2015-01-01},

journal = {Plant Signaling and Behavior},

volume = {10},

number = {5},

pages = {1-2},

publisher = {Taylor and Francis Inc.},

abstract = {Epigenetic modifications of the chromatin structure are crucial for many biological processes and act on genes during the development and germination of seeds. The spatial distribution of 3 epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 was investigated in ‘matured,’ ‘dry,’ ‘imbibed” and ‘germinating’ embryos of a model grass, Brachypodium. Our results indicate that the patterns of epigenetic modification differ in the various types of tissues of embryos that were analyzed. Such a tissue-specific manner of these modifications may be linked to the switch of the gene expression profiles in various organs of the developing embryo. © 2015 Taylor & Francis Group, LLC.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84916624831,

title = {Reconstructing the evolution of Brachypodium genomes using comparative chromosome painting},

author = { A. Betekhtin and G. Jenkins and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84916624831&doi=10.1371%2fjournal.pone.0115108&partnerID=40&md5=fa11d2743b8558bfd90660d8bae52e55},

doi = {10.1371/journal.pone.0115108},

issn = {19326203},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {12},

publisher = {Public Library of Science},

abstract = {Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n=10; B. sylvaticum 2n=18; B. pinnatum 2n=16; 2n=18; B. arbuscula 2n=18 and B. stacei 2n=20) three allotetraploids (B. pinnatum 2n=28; B. phoenicoides 2n=28 and B. hybridum 2n=30), and two species of unknown ploidy (B. retusum 2n=38 and B. mexicanum 2n=40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n =18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon. ©2014 Betekhtin et al.},

note = {38},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84904103572,

title = {Spatial distribution of epigenetic modifications in Brachypodium distachyon embryos during seed maturation and germination},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904103572&doi=10.1371%2fjournal.pone.0101246&partnerID=40&md5=73dbd091faa86c9270cf0ac270eeb31e},

doi = {10.1371/journal.pone.0101246},

issn = {19326203},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {7},

publisher = {Public Library of Science},

abstract = {Seed development involves a plethora of spatially and temporally synchronised genetic and epigenetic processes. Although it has been shown that epigenetic mechanisms, such as DNA methylation and chromatin remodelling, act on a large number of genes during seed development and germination, to date the global levels of histone modifications have not been studied in a tissue-specific manner in plant embryos. In this study we analysed the distribution of three epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 in 'matured', 'dry' and 'germinating' embryos of a model grass, Brachypodium distachyon (Brachypodium). Our results indicate that the abundance of these modifications differs considerably in various organs and tissues of the three types of Brachypodium embryos. Embryos from matured seeds were characterised by the highest level of H4K5ac in RAM and epithelial cells of the scutellum, whereas this modification was not observed in the coleorhiza. In this type of embryos H3K4me2 was most evident in epithelial cells of the scutellum. In 'dry' embryos H4K5ac was highest in the coleorhiza but was not present in the nuclei of the scutellum. H3K4me1 was the most elevated in the coleoptile but absent from the coleorhiza, whereas H3K4me2 was the most prominent in leaf primordia and RAM. In embryos from germinating seeds H4K5ac was the most evident in the scutellum but not present in the coleoptile, similarly H3K4me1 was the highest in the scutellum and very low in the coleoptile, while the highest level of H3K4me2 was observed in the coleoptile and the lowest in the coleorhiza. The distinct patterns of epigenetic modifications that were observed may be involved in the switch of the gene expression profiles in specific organs of the developing embryo and may be linked with the physiological changes that accompany seed desiccation, imbibition and germination. © 2014 Wolny et al.},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84899832143,

title = {Insight into the karyotype evolution of Brachypodium species using comparative chromosome barcoding},

author = { D. Idziak-Helmcke and I. Hazuka and B. Poliwczak and A. Wiszynska and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899832143&doi=10.1371%2fjournal.pone.0093503&partnerID=40&md5=f792b899dc05809b408cc66f5118db9d},

doi = {10.1371/journal.pone.0093503},

issn = {19326203},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {3},

publisher = {Public Library of Science},

abstract = {Paleogenomic studies based on bioinformatic analyses of DNA sequences have enabled unprecedented insight into the evolution of grass genomes. They have revealed that nested chromosome fusions played an important role in the divergence of modern grasses. Nowadays, studies on karyotype evolution based on the sequence analysis can also be effectively complemented by the fine-scale cytomolecular approach. In this work, we studied the karyotype evolution of small genome grasses using BAC-FISH based comparative chromosome barcoding in four Brachypodium species: diploid B. distachyon (2n = 10) and B. sylvaticum (2n = 18), diploid (2n = 18) and allopolyploid (2n = 28) B. pinnatum as well as B. phoenicoides (2n = 28). Using BAC clones derived from the B. distachyon genomic libraries for the chromosomes Bd2 and Bd3, we identified the descending dysploidy events that were common for diploids with x = 9 and B. distachyon as well as two nested chromosome fusions that were specific only for B. distachyon. We suggest that dysploidy events that are shared by different lineages of the genus had already appeared in their common ancestor. We also show that additional structural rearrangements, such as translocations and duplications, contributed to increasing genome diversification in the species analysed. No chromosomes structured exactly like Bd2 and Bd3 were found in B. pinnatum (2n = 28) and B. phoenicoides. The structure of Bd2 and Bd3 homeologues belonging to the two genomes in the allopolyploids resembled the structure of their counterparts in the 2n = 18 diploids. These findings reinforce the hypothesis which excludes B. distachyon as a potential parent for Eurasian perennial Brachypodium allopolyploids. Our cytomolecular data elucidate some mechanisms of the descending dysploidy in monocots and enable reconstructions of the evolutionary events which shaped the extant karyotypes in both the genus Brachypodium and in grasses as a whole. © 2014 Idziak et al.},

note = {26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84903594003,

title = {Update on the genomics and basic biology of Brachypodium. International Brachypodium Initiative (IBI)},

author = { P. Catalán and B. Chalhoub and V. Chochois and D.F. Garvin and R. Hasterok and A.J. Manzaneda and L.A.J. Mur and N. Pecchioni and S.K. Rasmussen and J.P. Vogel and A. Voxeur},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84903594003&doi=10.1016%2fj.tplants.2014.05.002&partnerID=40&md5=03aae969189038e1056ebc86c6e8d79b},

doi = {10.1016/j.tplants.2014.05.002},

issn = {13601385},

year  = {2014},

date = {2014-01-01},

journal = {Trends in Plant Science},

volume = {19},

number = {7},

pages = {414-418},

publisher = {Elsevier Ltd},

abstract = {The scientific presentations at the First International Bra-chypodium Conference (abstracts available at http://www.brachy2013.unimore.it) are evidence of the wide-spread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution; roots; abiotic and biotic stress; com-parative genomics; natural diversity; and cell walls) demonstrates that the Brachypodium research commu-nity has achieved a critical mass of tools and has transi-tioned from resource development to addressing biological questions, particularly those unique to grasses. © 2014 Elsevier Ltd.},

note = {48},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84884159498,

title = {Variability of stomata and 45S and 5S rDNAs loci characteristics in two species of Anthoxanthum genus: A. aristatum and A. odoratum (Poaceae)},

author = { M. Drapikowska and K. Susek and R. Hasterok and P. Szkudlarz and Z. Celka and B. Jackowiak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884159498&doi=10.1556%2fABiol.64.2013.3.8&partnerID=40&md5=b70e09f2ddc68845a321a5e3da929ba7},

doi = {10.1556/ABiol.64.2013.3.8},

issn = {02365383},

year  = {2013},

date = {2013-01-01},

journal = {Acta Biologica Hungarica},

volume = {64},

number = {3},

pages = {352-363},

abstract = {Diploid Anthoxanthum odoratum and tetraploid A. aristatum were compared with respect to stomatal guard cell lengths, and stomatal density at adaxial and abaxial surfaces of the lamina. Further, the genome size of both species was determined by flow cytometry, and the number as well as the chromosomal distribution of 5S and 45S rDNAs were examined using FISH with ribosomal DNA (rDNA) probes. The average length of stomatal guard cells in A. odoratum was shown to be greater than that for A. aristatum, but the ranges overlapped. Moreover, reduction in stomatal frequency was found at higher ploidy levels.The genome size was 6.863 pg/2C DNA for A. aristatum and 13.252 pg/2C DNA for A. odoratum. A. aristatum has four sites of 5S rDNA in its root-tip meristematic cells, whereas A. odoratum has six. Both species have six sites of 45S rDNA. Chromosomal localization of the rDNA varied, which suggests that chromosome rearrangements took place during Anthoxanthum genome evolution.},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84881192851,

title = {Tissue-Specific Epigenetic Modifications in Root Apical Meristem Cells of Hordeum vulgare},

author = { A.J. Brąszewska-Zalewska and E.A. Wolny and L. Smialek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84881192851&doi=10.1371%2fjournal.pone.0069204&partnerID=40&md5=0031f46a741a0280b8b236fbf4964b49},

doi = {10.1371/journal.pone.0069204},

issn = {19326203},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {7},

abstract = {Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac), histone H3 dimethylation (H3K4me2; H3K9me2) and DNA methylation (5mC) patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species. © 2013 Braszewska-Zalewska et al.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84878227807,

title = {Karyotyping of Brachypodium pinnatum (2n = 18) chromosomes using cross-species BAC-FISH},

author = { E.A. Wolny and W. Fidyk and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878227807&doi=10.1139%2fgen-2013-0012&partnerID=40&md5=aa498c8d9b7beadf868a5ece165d2678},

doi = {10.1139/gen-2013-0012},

issn = {08312796},

year  = {2013},

date = {2013-01-01},

journal = {Genome},

volume = {56},

number = {4},

pages = {239-243},

abstract = {Identification of individual chromosomes in a complement is usually a difficult task in the case of most plant species, especially for those with small, numerous, and morphologically uniform chromosomes. In this paper, we demonstrate that the landmarks produced by cross-species fluorescence in situ hybridisation (FISH) of Brachypodium distachyon derived bacterial artificial chromosome (BAC) clones can be used for discrimination of Brachypodium pinnatum (2n = 18) chromosomes. Selected sets of clones were hybridised in several sequential experiments performed on exactly the same chromosome spreads, using reprobing of cytological preparations. Analysis of the morphometric features of B. pinnatum chromosomes was performed to establish their total length, the position of centromeres, and the position of BAC-based landmarks in relation to the centromere, thereby enabling their effective karyotyping, which is a prerequisite for more complex study of the grass genome structure and evolution at the cytomolecular level. © 2013 Published by NRC Research Press.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84900340838,

title = {Epigenetic modifications of nuclei differ between root meristematic tissues of Hordeum vulgare},

author = { A.J. Brąszewska-Zalewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900340838&doi=10.4161%2fpsb.26711&partnerID=40&md5=f129ce337771fa55a6f7c49a8c6972a9},

doi = {10.4161/psb.26711},

issn = {15592316},

year  = {2013},

date = {2013-01-01},

journal = {Plant Signaling and Behavior},

volume = {8},

number = {10},

publisher = {Landes Bioscience},

abstract = {Recent studies on the role of epigenetic modifications during plant development emphasize the fact that both positional information and tissue specificity are essential factors that establish epigenetic marks and thus determine cell fate and differentiation processes. The root apical meristem (RAM), which contains stem cells and generates radial patterns of tissues, is an ideal model for studying the correlation between cell position and cell-type differentiation, with particular emphasis on the patterns, global levels, and landscapes of epigenetic modifications. To date, there has been no clear evidence for differential levels of histone and DNA modification across root meristematic tissues. Our study clearly indicates that levels of modifications with potential epigenetic effects vary between RAM tissues. Of particular interest is that histone H4 acetylation in the epidermis is not simply replication-dependent and probably plays a role in epidermal cell differentiation. © Landes Bioscience.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84861624557,

title = {Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapaB. oleracea monosomic alien addition lines},

author = { W.K. Heneen and M. Geleta and K. Brismar and Z. Xiong and J.C. Pires and R. Hasterok and A.I. Stoute and R.J. Scott and G.J. King and S. Kurup},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861624557&doi=10.1093%2faob%2fmcs052&partnerID=40&md5=a08663f38db0f62313c061a6253fb036},

doi = {10.1093/aob/mcs052},

issn = {03057364},

year  = {2012},

date = {2012-01-01},

journal = {Annals of Botany},

volume = {109},

number = {7},

pages = {1227-1242},

abstract = {Background and AimsBrassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes. MethodsA new batch of B. rapaB. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snows carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used. Key ResultsThe final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups. ConclusionsA complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker-assisted selection and breeding for yellow seeds. © The Author 2012. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.},

note = {24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84856757620,

title = {Evolution and taxonomic split of the model grass Brachypodium distachyon},

author = { P. Catalán and J. Müller and R. Hasterok and G. Jenkins and L.A.J. Mur and T. Langdon and A. Betekhtin and D. Siwińska and M. Pimentel and D. López-Alvarez},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856757620&doi=10.1093%2faob%2fmcr294&partnerID=40&md5=9bd59148b57fadf44df0564a599ed16b},

doi = {10.1093/aob/mcr294},

issn = {03057364},

year  = {2012},

date = {2012-01-01},

journal = {Annals of Botany},

volume = {109},

number = {2},

pages = {385-405},

abstract = {Background and Aims Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n= 10; 20; 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species. Methods Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF; trnLF) and five nuclear (ITS; ETS; CAL; DGAT; GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated. Key Results The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n= 10 and 2n= 20 cytotypes represent two different diploid taxa, whereas the 2n= 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n= 20 and 2n= 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n= 30 cytotype. The 2n= 20 lineage was older and mutated significantly faster than the 2n= 10 lineage and all the core perennial Brachypodium species. Conclusions The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B. distachyon for the 2n= 10 cytotype and have described two novel species as B. stacei and B. hybridum for, respectively, the 2n= 20 and 2n= 30 cytotypes. © 2011 The Author.},

note = {118},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84873267734,

title = {Intraspecific polymorphism of ribosomal DNA loci number and morphology in Brachypodium pinnatum and Brachypodium sylvaticum},

author = { E. Breda and E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873267734&doi=10.2478%2fs11658-012-0025-4&partnerID=40&md5=28d2364b5c42eb384ee1a12ab80631e5},

doi = {10.2478/s11658-012-0025-4},

issn = {14258153},

year  = {2012},

date = {2012-01-01},

journal = {Cellular and Molecular Biology Letters},

volume = {17},

number = {4},

pages = {526-541},

publisher = {BioMed Central Ltd.},

abstract = {The genus Brachypodium has become the target of extensive cytomolecular studies since one of its representatives, B. distachyon, has been accepted as a model plant for temperate cereals and forage grasses. Recent preliminary studies suggested that intraspecific rDNA polymorphism can occur in at least two members of the genus, B. sylvaticum and B. pinnatum, so the aim of this study was to further analyse this phenomenon. FISH with 25S rDNA and 5S rDNA probes was performed on somatic metaphase chromosomes, supplemented by the silver staining technique which distinguishes transcriptionally active from inactive 18S-5. 8S-25S rDNA loci. The number, size and chromosomal distribution of 5S rDNA loci were very constant: two loci were invariably observed in all studied diploid accessions of both species, while four 5S rDNA loci were present in the tetraploid B. pinnatum. In contrast to 5S rDNA loci, those of the 35S rDNA were more variable. Two or three loci were observed in the diploid B. pinnatum and four in tetraploid accessions. In chromosome complements of B. sylvaticum accessions from two to six 35S rDNA sites were detected. Regardless of total rDNA locus number, only two were transcriptionally active in diploid accessions of both species, while two or four were active in the tetraploid B. pinnatum. Additionally, the fluorescent CMA/DAPI banding method was used to identify the relation between rDNA sites and CMA+ bands. It was revealed that the number and chromosomal distribution of CMA+ bands are in congruence only with 35S rDNA loci which gave strong FISH signals. © 2012 Versita Warsaw and Springer-Verlag Wien.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-82955173028,

title = {DNA methylation patterns of Brachypodium distachyon chromosomes and their alteration by 5-azacytidine treatment},

author = { N. Borowska-Zuchowska and D. Idziak-Helmcke and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-82955173028&doi=10.1007%2fs10577-011-9243-2&partnerID=40&md5=4d75d4f1c9ba25362a473d9643a527d1},

doi = {10.1007/s10577-011-9243-2},

issn = {09673849},

year  = {2011},

date = {2011-01-01},

journal = {Chromosome Research},

volume = {19},

number = {8},

pages = {955-967},

abstract = {Sequential immunolocalisation of 5-methylcytosine (5-MeC) and fluorescence in situ hybridisation with chromosome-specific BAC clones were performed on Brachypodium distachyon mitotic metaphase chromosomes to determine specific DNA methylation patterns of each chromosome in the complement. In the majority of cells examined, chromosomes Bd4 and Bd5, which bear the loci of 5S and 35S ribosomal DNA, respectively, had characteristic 5-MeC patterns. In contrast, the distribution of 5-MeC along the metacentric chromosome pairs Bd1, Bd2 and Bd3 was more variable. There were numerous differences in distribution of methylated sites between homologous chromosomes as well as between chromosome arms. Some chromosome sites, such as pericentromeric regions, were highly methylated in all chromosomes. Additionally, the influence of a hypomethylating agent, 5-azacytidine, on B. distachyon chromosome methylation patterns was confirmed. It was found that some chromosome pairs underwent demethylation more easily than others, but there was no apparent regularity in demethylation of particular chromosome segments. © 2011 The Author(s).},

note = {13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-80054097796,

title = {Painting the chromosomes of Brachypodium-current status and future prospects},

author = { D. Idziak-Helmcke and A. Betekhtin and E.A. Wolny and K. Susek and J. Wright and M. Febrer and M.W. Bevan and G. Jenkins and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80054097796&doi=10.1007%2fs00412-011-0326-9&partnerID=40&md5=e58f0c0baf758f71c389d6c6eb612290},

doi = {10.1007/s00412-011-0326-9},

issn = {00095915},

year  = {2011},

date = {2011-01-01},

journal = {Chromosoma},

volume = {120},

number = {5},

pages = {469-479},

abstract = {Chromosome painting is one of the most powerful and spectacular tools of modern molecular cytogenetics, enabling complex analyses of nuclear genome structure and evolution. For many years, this technique was restricted to the study of mammalian chromosomes, as it failed to work in plant genomes due mainly to the presence of large amounts of repetitive DNA common to all the chromosomes of the complement. The availability of ordered, chromosome-specific BAC clones of Arabidopsis thaliana containing relatively little repetitive genomic DNA enabled the first chromosome painting in dicotyledonous plants. Here, we show for the first time chromosome painting in three different cytotypes of a monocotyledonous plant-the model grass, Brachypodium distachyon. Possible directions of further detailed studies are proposed, such as the evolution of grass karyotypes, the behaviour of meiotic chromosomes, and the analysis of chromosome distribution at interphase. © 2011 The Author(s).},

note = {46},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-79959813865,

title = {Exploiting the brachypodium tool box in cereal and grass research},

author = { L.A.J. Mur and J. Allainguillaume and P. Catalán and R. Hasterok and G. Jenkins and K. Susek and I. Thomas and J.P. Vogel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79959813865&doi=10.1111%2fj.1469-8137.2011.03748.x&partnerID=40&md5=e9bc03f40d54c2b3efea5f9032e73898},

doi = {10.1111/j.1469-8137.2011.03748.x},

issn = {0028646X},

year  = {2011},

date = {2011-01-01},

journal = {New Phytologist},

volume = {191},

number = {2},

pages = {334-347},

abstract = {It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.},

note = {113},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-79955523870,

title = {Compact genomes and complex evolution in the genus Brachypodium},

author = { E.A. Wolny and K. Susek and R. Hasterok and T. Langdon},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79955523870&doi=10.1007%2fs00412-010-0303-8&partnerID=40&md5=69284c1a124962d5ffd5895e0bd45961},

doi = {10.1007/s00412-010-0303-8},

issn = {00095915},

year  = {2011},

date = {2011-01-01},

journal = {Chromosoma},

volume = {120},

number = {2},

pages = {199-212},

abstract = {The temperate annual grass Brachypodium distachyon is a diploid species with a chromosome base number of 5. It is strikingly different from other Eurasian species of the genus, which are perennial and often polyploid, with the diploids typically having base numbers of 8 or 9. Previously, phylogenies indicated that B. distachyon split from the other species early in the evolution of the genus, while its genome sequence revealed that extensive synteny on a chromosomal scale had been maintained with rice, a tropical grass with a base number of 12. Here we show evidence that B. distachyon may have a homoploid origin, involving ancestral interspecific hybridisation, although it does not appear to be a component of any of the perennial Eurasian allopolyploids. Using a cytogenetic approach, we show that dysploidy in Brachypodium has not followed a simple progression. © 2010 Springer-Verlag.},

note = {32},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-78149437473,

title = {An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research},

author = { M. Febrer and J.L. Goicoechea and J. Wright and N. McKenzie and X. Song and J. Lin and K. Collura and M. Wissotski and Y. Yu and J.S.S. Ammiraju and E.A. Wolny and D. Idziak-Helmcke and A. Betekhtin and D. Kudrna and R. Hasterok and R.A. Wing and M.W. Bevan},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78149437473&doi=10.1371%2fjournal.pone.0013461&partnerID=40&md5=d1ddbfdfca8fbfda0316627d6007d582},

doi = {10.1371/journal.pone.0013461},

issn = {19326203},

year  = {2010},

date = {2010-01-01},

journal = {PLoS ONE},

volume = {5},

number = {10},

abstract = {The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation. © 2010 Febrer et al.},

note = {41},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-78149430690,

title = {Cytogenetic analysis of Hieracium transylvanicum (Asteraceae)},

author = { I. Tomasz and R. Hasterok and Z. Szeląg},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78149430690&doi=10.1080%2f00087114.2010.589726&partnerID=40&md5=25e7d628dc5cfa6300f345143b926419},

doi = {10.1080/00087114.2010.589726},

issn = {00087114},

year  = {2010},

date = {2010-01-01},

journal = {Caryologia},

volume = {63},

number = {2},

pages = {192-196},

abstract = {Hieracium transylvanicum is a relic species which occurs in refugial areas of south-eastern Europe. The structure of its karyotype, including determination of morphometric features of somatic metaphase chromosomes as well as the number and distribution of ribosomal DNA loci, was attempted using both classical chromosome staining and the FISH method with 25S rDNA and 5S rDNA probes. The cytotypes under study were collected from eight sites and did not vary significantly in terms of their karyotype organisation. All 11 specimens had the same chromosome number},

note = {14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-76749150030,

title = {Genome sequencing and analysis of the model grass Brachypodium distachyon},

author = { D. Idziak-Helmcke and R. Hasterok and J.P. Vogel and D.F. Garvin and T.C. Mockler and J. Schmutz and D. Rokhsar and M.W. Bevan and K. Barry and S. Lucas and M. Harmon-Smith and K. Lail and H. Tice and J. Grimwood and N. McKenzie and N. Huo and Y.Q. Gu and G.R. Lazo and O.D. Anderson and F.M. You and M.C. Luo and J. Dvorak and J. Wright and M. Febrer and E. Lindquist and M. Wang and S.E. Fox and H.D. Priest and S.A. Filichkin and S.A. Givan and D.W. Bryant and J.H. Chang and H. Wu and W. Wu and A.P. Hsia and P.S. Schnable and A. Kalyanaraman and B. Barbazuk and T.P. Michael and S.P. Hazen and J.N. Bragg and D. Laudencia-Chingcuanco and Y. Weng and G. Haberer and M. Spannagl and K. Mayer and T. Rattei and T. Mitros and S.J. Lee and J.K.C. Rose and L.A. Mueller and T.L. York and Authors. Other},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-76749150030&doi=10.1038%2fnature08747&partnerID=40&md5=2dd7dc679ba86d0d44e882c85e1adddd},

doi = {10.1038/nature08747},

issn = {00280836},

year  = {2010},

date = {2010-01-01},

journal = {Nature},

volume = {463},

number = {7282},

pages = {763-768},

publisher = {Nature Publishing Group},

abstract = {Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops. © 2010 Macmillan Publishers Limited. All rights reserved. 

Authors: Vogel, J.P.; Garvin, D.F.; Mockler, T.C.; Schmutz, J.; Rokhsar, D.; Bevan, M.W.; Barry, K.; Lucas, S.; Harmon-Smith, M.; Lail, K.; Tice, H.; Grimwood, J.; McKenzie, N.; Huo, N.; Gu, Y.Q.; Lazo, G.R.; Anderson, O.D.; You, F.M.; Luo, M.C.; Dvorak, J.; Wright, J.; Febrer, M.; Idziak-Helmcke, D.; Hasterok, R.; Lindquist, E.; Wang, M.; Fox, S.E.; Priest, H.D.; Filichkin, S.A.; Givan, S.A.; Bryant, D.W.; Chang, J.H.; Wu, H.; Wu, W.; Hsia, A.P.; Schnable, P.S.; Kalyanaraman, A.; Barbazuk, B.; Michael, T.P.; Hazen, S.P.; Bragg, J.N.; Laudencia-Chingcuanco, D.; Weng, Y.; Haberer, G.; Spannagl, M.; Mayer, K.; Rattei, T.; Mitros, T.; Lee, S.J.; Rose, J.K.C.; Mueller, L.A.; York, T.L.; Wicker, T.; Buchmann, J.P.; Tanskanen, J.; Schulman, A.H.; Gundlach, H.; Beven, M.; Costa De Oliveira, A.; Da C. Maia, L.; Belknap, W.; Jiang, N.; Lai, J.; Zhu, L.; Ma, J.; Sun, C.; Pritham, E.; Salse, J.; Murat, F.; Abrouk, M.; Bruggmann, R.; Messing, J.; Fahlgren, N.; Sullivan, C.M.; Carrington, J.C.; Chapman, E.J.; May, G.D.; Zhai, J.; Ganssmann, M.; Gurazada, S.G.R.; German, M.; Meyers, B.C.; Green, P.J.; Tyler, L.; Wu, J.; Thomson, J.; Chen, S.; Scheller, H.V.; Harholt, J.; Ulvskov, P.; Kimbrel, J.A.; Bartley, L.E.; Cao, P.; Jung, K.H.; Sharma, M.K.; Vega-Sanchez, M.; Ronald, P.; Dardick, C.D.; De Bodt, S.; Verelst, W.; Inzé, D.; Heese, M.; Schnittger, A.; Yang, X.; Kalluri, U.C.; Tuskan, G.A.; Hua, Z.; Vierstra, R.D.; Cui, Y.; Ouyang, S.; Sun, Q.; Liu, Z.; Yilmaz, A.; Grotewold, E.; Sibout, R.; Hematy, K.; Mouille, G.; Höfte, H.; Micheel, T.; Pelloux, J.; O'Connor, D.; Schnable, J.; Rowe, S.; Harmon, F.; Cass, C.L.; Sedbrook, J.C.; Byrne, M.E.; Walsh, S.; Higgins, J.; Li, P.; Brutnell, T.; Unver, T.; Budak, H.; Belcram, H.; Charles, M.; Chalhoub, B.; Baxter, I.},

note = {1363},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-78649700977,

title = {Ribosomal DNA, tri- and bi-partite pericentromeres in the permanent translocation heterozygote Rhoeo spathacea},

author = { H. Golczyk and R. Hasterok and M. Szklarczyk},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649700977&doi=10.2478%2fs11658-010-0034-0&partnerID=40&md5=e6ac185142d04f6312bb1f5577407bd7},

doi = {10.2478/s11658-010-0034-0},

issn = {14258153},

year  = {2010},

date = {2010-01-01},

journal = {Cellular and Molecular Biology Letters},

volume = {15},

number = {4},

pages = {651-664},

publisher = {BioMed Central Ltd.},

abstract = {High- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A3-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo. © 2010 Versita Warsaw and Springer-Verlag Wien.},

note = {11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-70349587942,

title = {Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives},

author = { E.A. Wolny and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-70349587942&doi=10.1093%2faob%2fmcp179&partnerID=40&md5=44169818ca6e826ec9ec1625450a9209},

doi = {10.1093/aob/mcp179},

issn = {03057364},

year  = {2009},

date = {2009-01-01},

journal = {Annals of Botany},

volume = {104},

number = {5},

pages = {873-881},

abstract = {Background and AimsBrachypodium is a small genus of temperate grasses that comprises 12-15 species. Brachypodium distachyon is now well established as a model species for temperate cereals and forage grasses. In contrast to B. distachyon, other members of the genus have been poorly investigated at the chromosome level or not at all.MethodsTwenty accessions comprising six species and two subspecies of Brachypodium were analysed cytogenetically. Measurements of nuclear genome size were made by flow cytometry. Chromosomal localization of 18-5·8-25S rDNA and 5S rDNA loci was performed by dual-colour fluorescence in situ hybridization (FISH) on enzymatically digested root-tip meristematic cells. For comparative phylogenetic analyses genomic in situ hybridization (GISH) applied to somatic chromosome preparations was used.Key ResultsAll Brachypodium species examined have rather small genomes and chromosomes. Their chromosome numbers and genome sizes vary from 2n = 10 and 0·631 pg/2C in B. distachyon to 2n = 38 and 2·57 pg/2C in B. retusum, respectively. Genotypes with 18 and 28 chromosomes were found among B. pinnatum accessions. GISH analysis revealed that B. pinnatum with 28 chromosomes is most likely an interspecific hybrid between B. distachyon (2n = 10) and B. pinnatum (2n = 18). Two other species, B. phoenicoides and B. retusum, are also allopolyploids and B. distachyon or a close relative seems to be one of their putative ancestral species. In chromosomes of all species examined the 45S rDNA loci are distally distributed whereas loci for 5S rDNA are pericentromeric. ConclusionsThe increasing significance of B. distachyon as a model grass emphasizes the need to understand the evolutionary relationships in the genus Brachypodium and to ensure consistency in the biological nomenclature of its species. Modern molecular cytogenetic techniques such as FISH and GISH are suitable for comparative phylogenetic analyses and may provide informative chromosome- and/or genome-specific landmarks.},

note = {54},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-44449177036,

title = {Cytogenetic evidence of nucleolar dominance in allotetraploid species of Brachypodium},

author = { D. Idziak-Helmcke and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-44449177036&doi=10.1139%2fG08-017&partnerID=40&md5=8317f921401953c82cc4fd3a97a8691c},

doi = {10.1139/G08-017},

issn = {08312796},

year  = {2008},

date = {2008-01-01},

journal = {Genome},

volume = {51},

number = {5},

pages = {387-391},

abstract = {Sequential silver staining and fluorescence in situ hybridization (FISH) were used to establish activity and number of 45S rDNA sites in meristematic root tip cells of 6 ecotypes of allotetraploid (2n = 4x = 30) species of Brachypodium and their putative ancestors, B. distachyon (2n = 2x = 10) and ABR114 (2n = 2x = 20). Using either total nuclear DNA of ABR114 or the ABR1-63-E6 BAC clone from a B. distachyon genomic library as an auxiliary probe, it was possible to distinguish by FISH between the two genomes composing the ecotypes of allotetraploid Brachypodium species and to determine unambiguously the parentage of both dominant and suppressed rRNA genes. Each of the diploid species possessed two rDNA loci, both transcriptionally active. The number of 45S rDNA sites in 6 ecotypes of allotetraploid Brachypodium species was always equal to the sum of loci present in their putative diploid parents. Two smaller sites were located in chromosomes corresponding to the ABR114 chromosomal set, and two larger ones in the chromosomes of B. distachyon origin. In all analyzed allotetraploid ecotypes, only rRNA genes belonging to the B. distachyon-like genome were transcriptionally active, while rDNA from the other parental genome was always suppressed. Thus the occurrence of nucleolar dominance in the allotetraploid (2n = 4x = 30) species of Brachypodium is demonstrated for the first time. © 2008 NRC.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-42449097595,

title = {Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research},

author = { D.F. Garvin and Y.Q. Gu and R. Hasterok and S.P. Hazen and G. Jenkins and T.C. Mockler and L.A.J. Mur and J.P. Vogel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-42449097595&doi=10.2135%2fcropsci2007.06.0332tpg&partnerID=40&md5=4ac344137456241bd4c5e9098cec8a85},

doi = {10.2135/cropsci2007.06.0332tpg},

issn = {0011183X},

year  = {2008},

date = {2008-01-01},

journal = {Crop Science},

volume = {48},

number = {SUPPL. 1},

pages = {S69-S84},

abstract = {Grass crop genomics research frequently is hindered by large genome sizes and polyploidy. While rice is an attractive system for grass genomics due to its small genome size and available genome sequence, it is not particularly well-suited as a robust model system for all grass crops. The wild grass species Brachypodium distachyon (L.) P. Beauv. (Brachypodium) has recently gained favor as a new model system for grass crop genomics research because it possesses a suite of biological traits desired in a model system. Further, it is more closely related to the large and diverse group of cool season grass crops than is either rice (Oryza sativa L.) or sorghum [Sorghum bicolor (L.) Moench.], the second grass crop species whose genome has been sequenced. Thus, by virtue both of its biological attributes and its evolutionary history, Brachypodium fills an important gap in grass crop genomics research. A surge in interest in Brachypodium has led to rapid and significant advances in the acquisition of knowledge and development of resources needed to exploit this species as a model system, including. the impending completion of a draft nuclear genome sequence of Brachypodium. Integration of diverse genetic and genomic resources developed or under development for Brachypodium with the genome sequence will encourage further adoption of this species as a bona fide model plant system. © Crop Science Society of America.},

note = {146},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-70249083748,

title = {Pericentromeric gc-rich chromatin in rhoeo (commelinaceae). Evidence from soma and germ-line},

author = { H. Golczyk and A.J. Joachimiak and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-70249083748&doi=10.1080%2f00087114.2008.10589651&partnerID=40&md5=3985e23aa885dc9b09e6390770fdca61},

doi = {10.1080/00087114.2008.10589651},

issn = {00087114},

year  = {2008},

date = {2008-01-01},

journal = {Caryologia},

volume = {61},

number = {4},

pages = {388-391},

abstract = {— CMA/DA/DAPI technique revealed the presence of GC-rich regions in mitotic/meiotic chromosomes and within meiotic collective chromocenters of permanent heterozygote Rhoeo spathacea (2n = 12). CMA-bands were detected within some NOR-related chromosome ends and within all twelve pericentromeric regions. It can not be excluded that GC-rich segments associated with AT-rich pericentromeric heterochromatin may serve as landmarks of the putative translocation breakpoints in this species. The persistence of two cytologically well-defned chromatin domains (AT and GC-rich) within pericentromeres of all chromosomes suggests spreading and homogenization of their sequences during evolution of Rhoeo karyotype. © 2008 Taylor & Francis Group, LLC.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-34347239708,

title = {BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment},

author = { G. Jenkins and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34347239708&doi=10.1038%2fnprot.2006.490&partnerID=40&md5=e3a80a110234354169e2adeafc5b6ff2},

doi = {10.1038/nprot.2006.490},

issn = {17542189},

year  = {2007},

date = {2007-01-01},

journal = {Nature Protocols},

volume = {2},

number = {1},

pages = {88-98},

abstract = {Fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) with large genomic DNA inserts as probes (BAC 'landing') is a powerful means by which eukaryotic genomes can be physically mapped and compared. Here we report a BAC landing protocol that has been developed specifically for the weedy grass species Brachypodium distachyon, which has been adopted recently by the scientific community as an alternative model for the temperate cereals and grasses. The protocol describes the preparation of somatic and meiotic chromosome substrates for FISH, the labeling of BACs, a chromosome mapping strategy, empirical conditions for optimal in situ hybridization and stringency washing, the detection of probes and the capturing and processing of images. The expected outcome of the protocol is the specific assignment of BACs containing single-copy inserts to one of the five linkage groups of the genome of this species. Once somatic or meiotic material is available, the entire protocol can be completed in about 3 d. The protocol has been customized empirically for B. distachyon and its near relatives, but it can be adapted with minor modifications to diverse plant species.},

note = {64},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-33744489394,

title = {Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization},

author = { R. Hasterok and A. Marasek and I.S. Donnison and I. Armstead and A. Thomas and I.P. King and E.A. Wolny and D. Idziak-Helmcke and J. Draper and G. Jenkins},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33744489394&doi=10.1534%2fgenetics.105.049726&partnerID=40&md5=fe1c6cb39d5cf5a72551bb8ff32a8943},

doi = {10.1534/genetics.105.049726},

issn = {00166731},

year  = {2006},

date = {2006-01-01},

journal = {Genetics},

volume = {173},

number = {1},

pages = {349-362},

abstract = {As part of an initiative to develop Brachypodium distachyon as a genomic "bridge" species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice. Copyright © 2006 by the Genetics Society of America.},

note = {104},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-33745318162,

title = {Multi-substrate chromosome preparations for high throughput comparative FISH},

author = { R. Hasterok and J. Dulawa and G. Jenkins and M. Leggett and T. Langdon},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745318162&doi=10.1186%2f1472-6750-6-20&partnerID=40&md5=ee8692475acee0e992e624bdcbb2f652},

doi = {10.1186/1472-6750-6-20},

issn = {14726750},

year  = {2006},

date = {2006-01-01},

journal = {BMC Biotechnology},

volume = {6},

abstract = {Background: A modification of a standard method of fluorescence in situ hybridisation (FISH) is described, by which a combination of several substrates and probes on single microscope slides enables more accurate comparisons of the distribution and abundance of chromosomal sequences and improves the relatively low throughput of standard FISH methods. Results: The utility and application of multi-colour, multi-substrate FISH is illustrated by the simultaneous physical mapping of retrotransposon sequences to three species of Avena, and single locus BAC (bacterial artificial chromosome) clones and rDNA probes to three species of Brachypodium, demonstrating how this would enable better understanding of complex phylogenetic relationships among some of the species belonging to these two genera. Conclusion: The results show that use of multi-substrate chromosome preparations significantly increases the utility of FISH in comparative analyses of the distribution and abundance of chromosomal sequences in closely related plant species. © 2006 Hasterok et al; licensee BioMed Central Ltd.},

note = {26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-31744436819,

title = {Comparative analysis of rDNA distribution in chromosomes of various species of Brassicaceae},

author = { R. Hasterok and E.A. Wolny and M. Hosiawa and M. Kowalczyk and S. Kulak-Ksiazczyk and T. Ksiązczyk and W.K. Heneen and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-31744436819&doi=10.1093%2faob%2fmcj031&partnerID=40&md5=0d82c13868701a373afa8f6633a37d79},

doi = {10.1093/aob/mcj031},

issn = {03057364},

year  = {2006},

date = {2006-01-01},

journal = {Annals of Botany},

volume = {97},

number = {2},

pages = {205-216},

abstract = {• Background and Aims: The Brassicaceae family encompasses numerous species of great agronomic importance, belonging to such genera, as Brassica, Raphanus, Sinapis and Armoracia. Many of them are characterized by extensive intraspecific diversity of phenotypes. The present study focuses on the polymorphism of number, appearance and chromosomal localization of ribosomal DNA (rDNA) sites and, when possible, in relation to polyploidy, in 42 accessions of Brassica species and ten accessions of Diplotaxis, Eruca, Raphanus and Sinapis species. • Methods: Chromosomal localization of ribosomal DNA was carried out using dual colour fluorescence in situ hybridization (FISH) with 5S rDNA and 25S rDNA sequences as probes on enzymatically digested root-tip meristematic cells. • Key Results: Loci for 5S and 18S-5.8S-25S rDNA were determined for the first time in six taxa, and previously unreported rDNA constellations were described in an additional 12 accessions. FISH revealed frequent polymorphism in number, appearance and chromosomal localization of both 5S and 25S rDNA sites. This phenomenon was most commonly observed in the A genome of Brassica, where it involves exclusively pericentromeric sites of 5S and 25S rRNA genes. The intraspecific polymorphism was between subspecies/varieties or within a variety or cultivar (i.e. interindividual). • Conclusions: The number of rDNA sites can differ up to 5-fold in species with the same chromosome number. In addition to the eight previously reported chromosomal types with ribosomal genes, three new variant types are described. The extent of polymorphism is genome dependent. Comparing the A, B and C genomes revealed the highest rDNA polymorphism in the A genome. The loci carrying presumably inactive ribosomal RNA genes are particularly prone to polymorphism. It can also be concluded that there is no obvious polyploidization-related tendency to reduce the number of ribosomal DNA loci in the allotetraploid species, when compared with their putative diploid progenitors. The observed differences are rather caused by the prevailing polymorphism within the diploids and allotetraploids. This would make it difficult to predict expected numbers of rDNA loci in natural polyploids. © The Author 2005. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.},

note = {114},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-28944441289,

title = {FISH and GISH analysis of Brassica genomes},

author = { R. Hasterok and T. Ksiązczyk and E.A. Wolny and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-28944441289&partnerID=40&md5=a5ca35de39bf658c5c304b07d941005b},

issn = {00015296},

year  = {2005},

date = {2005-01-01},

journal = {Acta Biologica Cracoviensia Series Botanica},

volume = {47},

number = {1},

pages = {185-192},

abstract = {Fluorescence and genomic in situ hybridization (FISH and GISH) methods were used for discrimination of Brassica genomes. The three diploid and three allotetraploid species of Brassica, known as the "U-triangle," represent an attractive model for molecular and cytological analysis of genome changes during phylogeny in the genus Brassica. The use of genomic DNA probes enabled unambiguous discrimination of the ancestral genomes in B. juncea and B. carinata, and was only partially successful inB. napus. GISH signals in all genomes were localized predominantly in pericentromeric regions of chromosomes. Simultaneous application of genomic and ribosomal DNA probes in multicolor GISH and FISH allowed identification of a significant number of chromosomes in the B. juncea complement. The study also revealed that species of Brassica possess Arabidopsis-type telomeric repeats which in all genomes occupied exclusively terminal, that is, telomeric, locations of chromosomes. © Polish Academy of Sciences, 2005.},

note = {21},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-22844431646,

title = {Molecular cytogenetic analysis of Brassica rapa-Brassica oleracea var. alboglabra monosomic addition lines},

author = { R. Hasterok and E.A. Wolny and S. Kulak and A. Zdziechiewicz and J. Małuszyńska and W.K. Heneen},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-22844431646&doi=10.1007%2fs00122-005-1942-7&partnerID=40&md5=21f499c1e9ea7ecb86be9b4f1acc8c7e},

doi = {10.1007/s00122-005-1942-7},

issn = {00405752},

year  = {2005},

date = {2005-01-01},

journal = {Theoretical and Applied Genetics},

volume = {111},

number = {2},

pages = {196-205},

abstract = {Interspecific alien chromosome addition lines can be very useful for gene mapping and studying chromosome homoeology between closely related species. In this study we demonstrate a simple but robust manner of identifying individual C-genome chromosomes (C5; C8 and C9) in the A-genome background through the simultaneous use of 5S and 25S ribosomal probes on mitotic and meiotic chromosomes of three different Brassica rapa-B. oleracea var. alboglabra monosomic addition lines. Sequential silver staining and fluorescence in situ hybridisation indicated that 18S-5.8S-25S rRNA genes on the additional chromosome C9 are expressed in the A-genome background. Meiotic behaviour of the additional chromosomes was studied in pollen mother cells at diakinesis and metaphase I. In all of the addition lines the alien chromosome was most frequently observed as a univalent. The alien chromosome C5, which carries an intercalary 5S rDNA locus, occasionally formed trivalents that involved either rDNA- or non rDNA-carrying chromosomes from the A genome. In the case of chromosomes C8 and C9, the most frequently observed intergenomic associations involved the regions occupied by 18S-5.8S-25S ribosomal RNA genes. It is possible that not all such associations represent true pairing but are remnants of nucleolar associations from the preceding interphase. Variations in the numbers and distribution of 5S and 25S rDNA sites between cultivars of B. oleracea, B. oleracea var. alboglabra and B. rapa are discussed. © Springer-Verlag 2005.},

note = {32},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-16344383382,

title = {Identification of individual chromosomes and parental genomes in Brassica juncea using GISH and FISH},

author = { J. Małuszyńska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-16344383382&doi=10.1159%2f000082414&partnerID=40&md5=29abf7e0b9ef49a39939cb133f7ba997},

doi = {10.1159/000082414},

issn = {14248581},

year  = {2005},

date = {2005-01-01},

journal = {Cytogenetic and Genome Research},

volume = {109},

number = {1-3},

pages = {310-314},

abstract = {The three diploid (B. nigra; B. oleracea; B. campestris) and three allotetraploid (B. carinata; B. juncea; B. napus) species of Brassica, known as the "U-triangle" are one of the best model systems for the study of polyploidy. Numerous molecular investigations have provided a wealth of new insights into the polyploid origin and changes during the evolution of Brassica, but there are still many controversial aspects of their relationship and evolution. Interpretation of genome changes during evolution requires individual chromosome identification within the genome and clear distinction of genomes within the allotetraploid. The aim of this study was to identify individual chromosomes of B. juncea (genome AABB; 2n = 4x = 36) and to determine their genomic origin. Fluorescence in situ hybridization with 5S and 45S rDNA probes enabled discrimination of a substantial number of chromosomes, providing chromosomal landmarks for 20 out of 36 chromosomes of B. juncea. Additionally, along with double target genomic in situ hybridization, it allowed assignment of all chromosomes to either the A or B genomes. Copyright © 2005 S. Karger AG, Basel.},

note = {46},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-19944402530,

title = {FISH-aimed karyotyping and characterization of Renner complexes in permanent heterozygote Rhoeo spathacea},

author = { H. Golczyk and R. Hasterok and A.J. Joachimiak},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-19944402530&doi=10.1139%2fg04-093&partnerID=40&md5=6b77a7b69dd27d2277e15ab56eded9cf},

doi = {10.1139/g04-093},

issn = {08312796},

year  = {2005},

date = {2005-01-01},

journal = {Genome},

volume = {48},

number = {1},

pages = {145-153},

abstract = {Fluorescence in situ hybridization (FISH) using 25S rDNA, 5S rDNA, and telomere sequences as probes was carried out in the complex permanent heterozygote Rhoeo spathacea. Telomere sites were exclusively terminal. All 10 25S rDNA loci were located distally and appeared transcriptionally active after silver staining. Six distal and 2 interstitial 5S rDNA sites were detected; 2 of the distal sites strictly colocalized with 25S rDNA loci. The 2 intercalary 5S rDNA loci occurred in short arms of 2 chromosomes that conjoined at meiosis. Chromosomes differed as to the amount of AT-rich centric heterochromatin, suggesting involvement of pericentromeric regions in translocations. The possibility of Robertsonian-like rearrangements was discussed. Double target FISH with ribosomal probes along with DAPI fluorescence gave the basis for full chromosome identification in mitosis. The 2 Renner complexes are structurally balanced, both having 5 25S and 4 5S rDNA sites. Centromere clustering, telomere association, a high number of NOR sites, and a strong tendency for formation of joint nucleoli contribute to the preservation of highly polarized Rabl arrangement at interphase. These findings were discussed in relation to meiotic catenation in Rhoeo. © 2005 NRC Canada.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-3142740749,

title = {Laying the cytotaxonomic foundations of a new model grass, Brachypodium distachyon (L.) beauv.},

author = { R. Hasterok and J. Draper and G. Jenkins},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-3142740749&doi=10.1023%2fB%3aCHRO.0000034130.35983.99&partnerID=40&md5=dbcc0731a42fa81a33b3a93e40e04bda},

doi = {10.1023/B:CHRO.0000034130.35983.99},

issn = {09673849},

year  = {2004},

date = {2004-01-01},

journal = {Chromosome Research},

volume = {12},

number = {4},

pages = {397-403},

abstract = {Brachypodium distachyon is a ubiquitous, temperate grass species which is being developed and exploited as an alternative model to rice, in order to gain access to important syntenic regions of the genomes of less tractable relatives such as wheat. As part of this initiative, this paper describes for the first time the cytotaxonomy of members of the polyploid series of this species, and challenges the assumption that the series evolved simply by chromosome doubling. In situ hybridization using genomic DNA probes and rDNA markers uncovers a hybrid origin of several of the polyploid ecotypes, and sheds light upon the complex evolution of this species and its close relatives.},

note = {85},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-1842471019,

title = {Determination by GISH and FISH of hybrid status in Lilium},

author = { A. Marasek and R. Hasterok and K. Wiejacha and T. Orlikowska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-1842471019&doi=10.1111%2fj.1601-5223.2004.01721.x&partnerID=40&md5=d1ab1e2921b92d3417b0ebdd355b2fa4},

doi = {10.1111/j.1601-5223.2004.01721.x},

issn = {00180661},

year  = {2004},

date = {2004-01-01},

journal = {Hereditas},

volume = {140},

number = {1},

pages = {1-7},

abstract = {In the genus Lilium, plants obtained from crosses, especially between distant relatives, are not always hybrids because embryos can develop as a result of apomixis. These plants constitute genetic material of the maternal parent only. In this study, verification of hybrid status of plants which have been obtained from the crosses 'Marco Polo' x Lilium henryi and 'Expression' x L. henryi was performed through the use of cytological and molecular cytogenetic methods. According to cytological analyses, all genotypes tested had 2n = 2x = 24 chromosomes. Genomic in situ hybridisation (GISH) was used for hybrid verification. In hybrid plants, this method distinguished all paternal and maternal chromosomes at the stage of somatic metaphase and prophase. For GISH, paternal genomic DNA was used as a probe and maternal DNAs were used as blocks. Fluorescence in situ hybridisation (FISH) with 5S rDNA and 25S rDNA probes was used as the second method of hybrid verification. Selected chromosome markers based on genome-specific localisation of rDNA loci were used for analysis of the F1 hybrids obtained from the crosses 'Marco Polo' x L. henryi and 'Expression' x L. henryi. The presence of marker chromosomes characteristic for each of the paternal genotypes was a confirmation that the plants obtained were hybrids.},

note = {62},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0142028915,

title = {Molecular cytogenetic analysis of genome structure in Lupinus angustifolius and Lupinus cosentinii},

author = { I. Hajdera and D. Siwińska and R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0142028915&doi=10.1007%2fs00122-003-1303-3&partnerID=40&md5=5a3f91ea2499ae60339d064216c56cbb},

doi = {10.1007/s00122-003-1303-3},

issn = {00405752},

year  = {2003},

date = {2003-01-01},

journal = {Theoretical and Applied Genetics},

volume = {107},

number = {6},

pages = {988-996},

abstract = {Molecular cytogenetic analysis of Lupinus angustifolius and Lupinus cosentinii was performed using flow cytometry, fluorescence in situ hybridisation (FISH) and differential chromosome staining. Genome size was determined as 2.07 pg for L. angustifolius and 1.54 pg for L. cosentinii. Analysis of nuclear DNA amount in cells during plant development has shown endopolyploidisation in different organs. The highest level of endopolyploidy was in cotyledons and reached 32C in L. angustifolius and 64C in L. cosentinii. Both of the investigated Lupinus species belong to the polysomatic type of plants. Double FISH with rDNA probes provided chromosomal landmarks for 10 out of 40 chromosomes for L. angustifolius and 8 out of 32 chromosomes for L. cosentinii. In L. angustifolius, the number and localisation of 25S rDNA hybridisation signals precisely corresponded to the chromomycin A3 (CMA +) bands, while in L. cosentinii both 25S and 5S rDNA loci overlapped with CMA+ bands. Silver staining revealed that only 45S rRNA genes located in secondary constriction regions were transcriptionally active. FISH with Arabidopsis-type telomeric arrays revealed the presence of signals at termini of all chromosomes. Despite the application of different DNA probes for FISH and different chromosome staining, a relatively small proportion of chromosomes in the Lupinus karyotypes can be distinguished. Identification of all chromosomes requires the use of more chromosome-specific markers.},

note = {55},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0037356448,

title = {A high-copy-number CACTA family transposon in temperate grasses and cereals},

author = { T. Langdon and G. Jenkins and R. Hasterok and R.N. Jones and I.P. King},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037356448&partnerID=40&md5=d8fad84594d5d7a5c42b60be3a902ac1},

issn = {00166731},

year  = {2003},

date = {2003-01-01},

journal = {Genetics},

volume = {163},

number = {3},

pages = {1097-1108},

abstract = {A lineage of CACTA family transposons has been identified in temperate grasses and cereals, and a full-length representative of the subfamily from Lolium perenne has been sequenced. Both the size and internal organization of the L. perenne element are typical of other CACTA family elements but its high copy number and strong conservation are unexpected. Comparison with homologs in other species suggests that this lineage has adopted a distinct and novel evolutionary strategy, which has allowed it to maintain its presence in genomes over long periods of time.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0036822767,

title = {Erratum: Karyotyping of Brassica amphidiploids using 5S and 25S rDNA as chromosome markers (Hereditas (2002) 136 (144-150))},

author = { S. Kulak and R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036822767&doi=10.1034%2fj.1601-5223.2002.1370112.x&partnerID=40&md5=98f9cc6cc47c50b11a272253165acd68},

doi = {10.1034/j.1601-5223.2002.1370112.x},

issn = {00180661},

year  = {2002},

date = {2002-01-01},

journal = {Hereditas},

volume = {137},

number = {1},

pages = {79-80},

abstract = {[No abstract available]},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0036618989,

title = {Karyotyping of Brassica amphidiploids using 5S and 25S rDNA as chromosome markers},

author = { S. Kulak and R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036618989&doi=10.1034%2fj.1601-5223.2002.1360209.x&partnerID=40&md5=5c54eeaa01ea33ce1bea63700d3f74d1},

doi = {10.1034/j.1601-5223.2002.1360209.x},

issn = {00180661},

year  = {2002},

date = {2002-01-01},

journal = {Hereditas},

volume = {136},

number = {2},

pages = {144-150},

abstract = {Species of Brassica have small, morphologically similar chromosomes, which makes karyotyping difficult using conventional cytogenetic methods. Molecular cytogenetic methods, like fluorescence in situ hybridisation (FISH) have the potential to improve karyotyping through the use of chromosome- or genome-specific markers. Simultaneous application of more than one DNA probe can greatly enrich the results obtained compared with separate single target FISH experiments. This paper demonstrates the use of multicolour fluorescence in situ hybridisation with 5S and 25S rDNA for karyotyping three amphidiploid species: B. napus, B. juncea and B. carinata. Using this method, it was possible to identify eight out of nineteen pairs of chromosomes in B. napus, ten out of eighteen pairs in B. juncea and six out of sixteen pairs in B. carinata. Additionally, rDNA sites allow the determination of the genomic origin of all marked chromosomes in B. napus and B. juncea.},

note = {36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0036316185,

title = {Combinatorial labelling of DNA probes enables multicolour fluorescence in situ hybridisation in plants},

author = { R. Hasterok and T. Langdon and S. Taylor and G. Jenkins},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036316185&partnerID=40&md5=b27b1f21824f76863d4bf235d63c5299},

issn = {02398508},

year  = {2002},

date = {2002-01-01},

journal = {Folia Histochemica et Cytobiologica},

volume = {40},

number = {3},

pages = {319-323},

publisher = {Polish Histochemical and Cytochemical Society},

abstract = {This paper demonstrates a simple but effective use of combinatorial probes to label plant chromosomes by multicolor fluorescence in situ hybridisation (FISH). Three different DNA probes were labelled with only two different fluorophores, hybridised to somatic metaphase chromosomes of Secale cereale and Triticum aestivum, simultaneously visualised, and unequivocally distinguished in a single FISH experiment. Combinatorial labelling can augment karyotypical investigations, physical mapping of chromosomes and other analyses in plants based upon FISH.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0034823385,

title = {Ribosomal DNA is an effective marker of Brassica chromosomes},

author = { R. Hasterok and G. Jenkins and T. Langdon and R.N. Jones and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034823385&doi=10.1007%2fs001220100653&partnerID=40&md5=b00c44157ef6b292e357473efee1d034},

doi = {10.1007/s001220100653},

issn = {00405752},

year  = {2001},

date = {2001-01-01},

journal = {Theoretical and Applied Genetics},

volume = {103},

number = {4},

pages = {486-490},

abstract = {Simultaneous fluorescence in situ hybridisation with 5S and 25S rDNA probes enables the discrimination of a substantial number of chromosomes of the complement of all diploid and tetraploid Brassica species of the "U-triangle", and provides new chromosomal landmarks for the identification of some chromosomes of this genus which were hitherto indistinguishable. Twelve out of 20 chromosomes can be easily identified in diploid Brassica campestris (AA genome), eight out of 16 in Brassica nigra (BB genome), and six out of 18 in Brassica oleracea (CC genome). Furthermore, just two rDNA markers permit 20 out of 36 chromosomes to be distinguished and assigned to either the A or B genomes of the allotetraploid Brassica juncea, and 18 out of 38 chromosomes identified and assigned to the A or C genomes of the allotetraploid Brassica napus. The number of chromosomes bearing rDNA sites in the tetraploids is not in all cases simply the sum of the numbers of sites in their diploid ancestors. This observation is discussed in terms of the phylogeny and variability within the genomes of the species of this group.},

note = {114},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85047683772,

title = {Brachypodium distachyon. A new model system for functional genomics in grasses},

author = { J. Draper and L.A.J. Mur and G. Jenkins and G.C. Ghosh-Biswas and P. Bablak and R. Hasterok and A.P.M. Routledge},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047683772&doi=10.1104%2fpp.010196&partnerID=40&md5=3102d0e8a49a0752486b7022aa201d23},

doi = {10.1104/pp.010196},

issn = {00320889},

year  = {2001},

date = {2001-01-01},

journal = {Plant Physiology},

volume = {127},

number = {4},

pages = {1539-1555},

publisher = {American Society of Plant Biologists},

abstract = {A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.},

note = {420},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0034353909,

title = {Cytogenetic analysis of diploid Brassica species},

author = { R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034353909&partnerID=40&md5=33f677ae67f3694f21f49a7f74f8da28},

issn = {00015296},

year  = {2000},

date = {2000-01-01},

journal = {Acta Biologica Cracoviensia Series Botanica},

volume = {42},

number = {1},

pages = {145-153},

abstract = {The chromosomes of Brassica species are small and poorly differentiated, and their identification is extremely difficult using conventional cytogenetic methods. Progress in molecular analysis of Brassica species requires cytogenetic maps of their chromosomes. Chromosome-specific markers are needed to distinguish particular pairs of homologous chromosomes and for karyotyping. In this study, three morphological groups of chromosomes in B. campestris (genome A) and B. oleracea (genome C) and two in B. nigra (genome B) were distinguished by the morphometric features of the chromosomes, based upon arm ratio and absolute length. Using fluorescence in situ hybridization and differential stainings it was possible to establish further markers for five pairs of chromosomes in genome A, three in genome B and two in genome C, and to present idiograms of the chromosomes for three diploid Brassica species. However, for clear identification of all chromosome pairs more cytogenetic markers are needed.},

note = {16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0002947010,

title = {Cytogenetic markers of Brassica napus L. chromosomes},

author = { R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0002947010&partnerID=40&md5=a9bd6862439ef126d32244c28da64f76},

issn = {12341983},

year  = {2000},

date = {2000-01-01},

journal = {Journal of Applied Genetics},

volume = {41},

number = {1},

pages = {1-9},

abstract = {Brassica napus has relatively small and poorly differentiated chromosomes. The total length, arm ratio and localisation of 18S-5.8S-26S rRNA genes formed the basis for the preparation of the ideogram of metaphase chromosomes. The morphometric features of the B. napus chromosomes allow for their classification into three morphological groups, but it is difficult to distinguish particular chromosome pairs within the groups. rRNA genes are present in 12 chromosomes of the diploid complement and are located in three chromosomal positions: secondary constrictions, terminal and pericentromeric regions. All rDNA loci at the secondary constriction are active. The signals of in situ hybridisation with rDNA co-localise with CMA positive bands in most of the loci. It was found that rRNA genes are good markers for some B. napus chromosomes, but still more cytogenetic markers are needed for the identification of all chromosome pairs.},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0033858050,

title = {Nucleolar dominance does not occur in root tip cells of allotetraploid Brassica species},

author = { R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033858050&doi=10.1139%2fg00-005&partnerID=40&md5=588fc389d10288f5cb88734a4b82a6f2},

doi = {10.1139/g00-005},

issn = {08312796},

year  = {2000},

date = {2000-01-01},

journal = {Genome},

volume = {43},

number = {3},

pages = {574-579},

publisher = {National Research Council of Canada},

abstract = {Using in situ hybridization and silver staining methods, the numbers of active and inactive rDNA loci have been established for three allotetraploid species of Brassica (B. napus, B. carinata, and B. juncea) and their diploid ancestors (B. campestris, B. nigra, and B. oleracea). The allotetraploid species have chromosome numbers equal to the sum of the numbers in their diploid relatives, but have fewer rDNA loci. All species investigated have lower numbers of active NORs (AgNORs, nucleolar organizer regions) compared with the numbers of rDNA sites revealed by in situ hybridization. The number of active rDNA loci of the allotetraploid species is equal to the number of AgNORs in their diploid ancestors, indicating the absence of nucleolar dominance in amphidiploid Brassica species, at least in root meristematic cells.},

note = {44},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-0033786413,

title = {Different rRNA gene expression in primary and adventitious roots of Allium cepa L.},

author = { R. Hasterok and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033786413&partnerID=40&md5=3356e643e4975528ef7332936b63f6a6},

issn = {02398508},

year  = {2000},

date = {2000-01-01},

journal = {Folia Histochemica et Cytobiologica},

volume = {38},

number = {4},

pages = {181-184},

publisher = {Polish Histochemical and Cytochemical Society},

abstract = {Sequentially used silver staining and in situ hybridization allowed to estimate the number of rDNA loci and their activity in meristematic cells of Allium cepa roots. In primary roots, obtained from germinated seeds, the rDNA probe hybridized with four chromosomes and showed four strong sites of hybridization. All of them displayed very clear positive silver staining. In cells of adventitious roots, from bulbs, only one pair of rRNA gene loci was active and after in situ hybridization showed strong signals while two other sites were very weak. The results indicate different transcriptional rRNA gene activity in meristematic cells of roots of different developmental origin. The reduction of the number of active rRNA loci can be the result of DNA methylation but the reduction mechanism of in situ hybridization sites in adventitious roots of Allium cepa remains an open question.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}