@article{2-s2.0-85182449811,

title = {Phaseolus vulgaris mutants reveal variation in the nuclear genome},

author = { N.B. Tomlekova and D. Idziak-Helmcke and P. Franke and M. Rojek-Jelonek and J. Kwaśniewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85182449811&doi=10.3389%2ffpls.2023.1308830&partnerID=40&md5=127d1d9cf9486b4ffecc9560104be662},

doi = {10.3389/fpls.2023.1308830},

issn = {1664462X},

year  = {2023},

date = {2023-01-01},

journal = {Frontiers in Plant Science},

volume = {14},

publisher = {Frontiers Media SA},

abstract = {Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean. Copyright © 2024 Tomlekova, Idziak-Helmcke, Franke, Rojek-Jelonek and Kwasniewska.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85132104188,

title = {Unraveling the DNA Methylation in the rDNA Foci in Mutagen-Induced Brachypodium distachyon Micronuclei},

author = { A.W. Bara-Halama and D. Idziak-Helmcke and J. Kwaśniewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85132104188&doi=10.3390%2fijms23126797&partnerID=40&md5=c00a2c7c8f2b040a71ae078f29684e7e},

doi = {10.3390/ijms23126797},

issn = {16616596},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {12},

publisher = {MDPI},

abstract = {Many years have passed since micronuclei were first observed then accepted as an indicator of the effect of mutagens. However, the possible mechanisms of their formation and elimination from the cell are still not fully understood. Various stresses, including mutagens, can alter gene expression through changes in DNA methylation in plants. In this study we demonstrate for the first time DNA methylation in the foci of 5S and 35S rDNA sequences in individual Brachypodium distachyon micronuclei that are induced by mutagenic treatment with maleic acid hydrazide (MH). The impact of MH on global epigenetic modifications in nuclei and micronuclei has been studied in plants before; however, no in situ analyses of DNA methylation in specific DNA sequence sites are known. To address this problem, we used sequential immunodetection of 5-methylcytosine and fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes on the non-dividing cells of B. distachyon. Such investigations into the presence or absence of DNA methylation within specific DNA sequences are extremely important in plant mutagenesis in the light of altering gene expression. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121867264,

title = {Novel visual analytics approach for chromosome territory analysis},

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

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121867264&doi=10.7717%2fpeerj.12661&partnerID=40&md5=ca61cb20b6d7b701a8e5eca0cb488717},

doi = {10.7717/peerj.12661},

issn = {21678359},

year  = {2021},

date = {2021-01-01},

journal = {PeerJ},

volume = {9},

publisher = {PeerJ Inc.},

abstract = {This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus. Copyright © 2021 Tkacz et al.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85091301980,

title = {Functioning of the photosynthetic apparatus in response to drought stress in oat × maize addition lines},

author = { K. Juzoń and D. Idziak-Helmcke and M. Rojek-Jelonek and T. Warzecha and M. Warchoł and I. Czyczyło-Mysza and K. Dziurka and E. Skrzypek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85091301980&doi=10.3390%2fijms21186958&partnerID=40&md5=e24e6608ea7223d21a47713fc50d2402},

doi = {10.3390/ijms21186958},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-25},

publisher = {MDPI AG},

abstract = {The oat × maize chromosome addition (OMA) lines, as hybrids between C3 and C4 plants, can potentially help us understand the process of C4 photosynthesis. However, photosynthesis is often affected by adverse environmental conditions, including drought stress. Therefore, to assess the functioning of the photosynthetic apparatus in OMA lines under drought stress, the chlorophyll content and chlorophyll a fluorescence (CF) parameters were investigated. With optimal hydration, most of the tested OMA lines, compared to oat cv. Bingo, showed higher pigment content, and some of them were characterized by increased values of selected CF parameters. Although 14 days of drought caused a decrease of chlorophylls and carotenoids, only slight changes in CF parameters were observed, which can indicate proper photosynthetic efficiency in most of examined OMA lines compared to oat cv. Bingo. The obtained data revealed that expected changes in hybrid functioning depend more on the specific maize chromosome and its interaction with the oat genome rather than the number of retained chromosomes. OMA lines not only constitute a powerful tool for maize genomics but also are a source of valuable variation in plant breeding, and can help us to understand plant susceptibility to drought. Our research confirms more efficient functioning of hybrid photosynthetic apparatus than oat cv. Bingo, therefore contributes to raising new questions in the fields of plant physiology and biochemistry. Due to the fact that the oat genome is not fully sequenced yet, the mechanism of enhanced photosynthetic efficiency in OMA lines requires further research. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85086754146,

title = {3-D nucleus architecture in oat × maize addition lines},

author = { D. Idziak-Helmcke and T. Warzecha and M. Sowa and M. Warchoł and K. Dziurka and I. Czyczyło-Mysza and E. Skrzypek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086754146&doi=10.3390%2fijms21124280&partnerID=40&md5=7449a31e7812d53321461bb61b5ad477},

doi = {10.3390/ijms21124280},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {12},

pages = {1-22},

publisher = {MDPI AG},

abstract = {The nucleus architecture of hybrid crop plants is not a well-researched topic, yet it can have important implications for their genetic stability and usefulness in the successful expression of agronomically desired traits. In this work we studied the spatial distribution of introgressed maize chromatin in oat × maize addition lines with the number of added maize chromosomes varying from one to four. The number of chromosome additions was confirmed by genomic in situ hybridization (GISH). Maize chromosome-specific simple sequence repeat (SSR) markers were used to identify the added chromosomes. GISH on 3-D root and leaf nuclei was performed to assess the number, volume, and position of the maize-chromatin occupied regions. We revealed that the maize chromosome territory (CT) associations of varying degree prevailed in the double disomic lines, while CT separation was the most common distribution pattern in the double monosomic line. In all analyzed lines, the regions occupied by maize CTs were located preferentially at the nuclear periphery. A comparison between the tissues showed that the maize CTs in the leaf nuclei are positioned closer to the center of the nucleus than in the root nuclei. These findings shed more light on the processes that shape the nucleus architecture in hybrids. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85049247123,

title = {Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)},

author = { E. Skrzypek and T. Warzecha and A. Noga and M. Warchoł and I. Czyczyło-Mysza and K. Dziurka and I. Marcińska and K. Kapłoniak and A. Sutkowska and Z. Nita and K. Werwińska and D. Idziak-Helmcke and M. Rojek-Jelonek and M. Hosiawa-Barańska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049247123&doi=10.7717%2fpeerj.5107&partnerID=40&md5=0325cd81ea9a5e47f329ef405e3a02ce},

doi = {10.7717/peerj.5107},

issn = {21678359},

year  = {2018},

date = {2018-01-01},

journal = {PeerJ},

volume = {2018},

number = {6},

publisher = {PeerJ Inc.},

abstract = {Background. The oat×maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods. Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande- 1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results. A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA-one maize chromosome, and one OMA-four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1-102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1-343 (in total 3;758). Obtained DH and OMA lines were fertile and produced seeds. Discussion. In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes. © 2018 Skrzypek et al.},

note = {4},

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-s2.0-84948394533,

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-s2.0-84899832143,

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-s2.0-82955173028,

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-s2.0-78149437473,

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-s2.0-76749150030,

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-s2.0-44449177036,

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-s2.0-39749149700,

title = {Pair correlation function analysis of 5-(4-hexadecyloxyphenyl)-10,15,20-tri(4-pyridyl)porphyrin and 5-(4-methoxycarbonylphenyl)-10,15,20-tri(4-pyridyl)porphyrin},

author = { A. Pasewicz and D. Idziak-Helmcke and J. Kołoczek and P. Kuś and R. Wrzalik and T. Fennell and V. Honkimäki and A. Ratuszna and A. Burian},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-39749149700&doi=10.1016%2fj.molstruc.2007.04.025&partnerID=40&md5=e3df5501f51a93467be974284eca5fe8},

doi = {10.1016/j.molstruc.2007.04.025},

issn = {00222860},

year  = {2008},

date = {2008-01-01},

journal = {Journal of Molecular Structure},

volume = {875},

number = {1-3},

pages = {167-172},

abstract = {The high-energy X-ray diffraction measurements were carried out for 5-(4-hexadecyloxyphenyl)-10,15,20-tri(4-pyridyl)porphyrin and 5-(4-methoxycarbonylphenyl)-10,15,20-tri(4-pyridyl)porphyrin. The scattered intensities were recorded on the ID15B beam line at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. An incident beam-energy of 90.45 keV was used, corresponding to a wavelength of 0.1374 Å. The pair correlation functions were obtained from the measured intensities via the Fourier transform. The density-functional theory was used to construct structural models of both molecules consisting of the atomic Cartesian coordinates. For these models the pair correlation functions were computed. The constructed models reproduce satisfactorily features of the experimental pair correlation functions. The results of such simulations are discussed in the framework of the density-functional approach. © 2008.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-34548496490,

title = {Molecular structure of 5,10,15,20-tetra(1-naphthyl)porphyrin and 5,10-di(4-hexadecyloxyphenyl)-15,20-di(4-pyridyl)porphyrin studied by high-energy X-ray diffraction},

author = { D. Idziak-Helmcke and A. Pasewicz and J. Kołoczek and P. Kuś and R. Wrzalik and T. Fennell and V. Honkimäki and A. Ratuszna and A. Burian},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34548496490&doi=10.1016%2fj.cplett.2007.07.050&partnerID=40&md5=bcc994525aaac92264b69b4c881516e0},

doi = {10.1016/j.cplett.2007.07.050},

issn = {00092614},

year  = {2007},

date = {2007-01-01},

journal = {Chemical Physics Letters},

volume = {446},

number = {1-3},

pages = {36-42},

abstract = {The molecular structure of the 5,10,15,20-tetra(1-naphthyl)porphyrin and 5,10-di(4-hexadecyloxyphenyl)-15,20-di(4-pyridyl)porphyrin were studied using high-energy X-ray diffraction (ID15-B beam line) at ESRF, Grenoble, France. The energy of the incident photons was 90.45 keV. Two-dimensional detector was used. The intensity data were converted to the pair correlation function via the Fourier transform. The theoretical pair correlation functions were simulated using the density functional theory and compared with the experimental data. Obtained results indicate that the used experimental technique together with the applied interpretation method can be regarded as efficient tools for the determination of the atomic arrangement in molecules of such kind. © 2007 Elsevier B.V. All rights reserved.},

note = {4},

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}

}