Publications by authors named "Heidrun Gundlach"

49 Publications

Multiple wheat genomes reveal global variation in modern breeding.

Authors:
Sean Walkowiak Liangliang Gao Cecile Monat Georg Haberer Mulualem T Kassa Jemima Brinton Ricardo H Ramirez-Gonzalez Markus C Kolodziej Emily Delorean Dinushika Thambugala Valentyna Klymiuk Brook Byrns Heidrun Gundlach Venkat Bandi Jorge Nunez Siri Kirby Nilsen Catharine Aquino Axel Himmelbach Dario Copetti Tomohiro Ban Luca Venturini Michael Bevan Bernardo Clavijo Dal-Hoe Koo Jennifer Ens Krystalee Wiebe Amidou N'Diaye Allen K Fritz Carl Gutwin Anne Fiebig Christine Fosker Bin Xiao Fu Gonzalo Garcia Accinelli Keith A Gardner Nick Fradgley Juan Gutierrez-Gonzalez Gwyneth Halstead-Nussloch Masaomi Hatakeyama Chu Shin Koh Jasline Deek Alejandro C Costamagna Pierre Fobert Darren Heavens Hiroyuki Kanamori Kanako Kawaura Fuminori Kobayashi Ksenia Krasileva Tony Kuo Neil McKenzie Kazuki Murata Yusuke Nabeka Timothy Paape Sudharsan Padmarasu Lawrence Percival-Alwyn Sateesh Kagale Uwe Scholz Jun Sese Philomin Juliana Ravi Singh Rie Shimizu-Inatsugi David Swarbreck James Cockram Hikmet Budak Toshiaki Tameshige Tsuyoshi Tanaka Hiroyuki Tsuji Jonathan Wright Jianzhong Wu Burkhard Steuernagel Ian Small Sylvie Cloutier Gabriel Keeble-Gagnère Gary Muehlbauer Josquin Tibbets Shuhei Nasuda Joanna Melonek Pierre J Hucl Andrew G Sharpe Matthew Clark Erik Legg Arvind Bharti Peter Langridge Anthony Hall Cristobal Uauy Martin Mascher Simon G Krattinger Hirokazu Handa Kentaro K Shimizu Assaf Distelfeld Ken Chalmers Beat Keller Klaus F X Mayer Jesse Poland Nils Stein Curt A McCartney Manuel Spannagl Thomas Wicker Curtis J Pozniak

Nature 2020 12 25;588(7837):277-283. Epub 2020 Nov 25.

Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome, and the lack of genome-assembly data for multiple wheat lines. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
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http://dx.doi.org/10.1038/s41586-020-2961-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759465PMC
December 2020

The barley pan-genome reveals the hidden legacy of mutation breeding.

Nature 2020 12 25;588(7837):284-289. Epub 2020 Nov 25.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
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http://dx.doi.org/10.1038/s41586-020-2947-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759462PMC
December 2020

European maize genomes highlight intraspecies variation in repeat and gene content.

Nat Genet 2020 09 27;52(9):950-957. Epub 2020 Jul 27.

Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.

The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today's highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.
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http://dx.doi.org/10.1038/s41588-020-0671-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7467862PMC
September 2020

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools.

Genome Biol 2019 12 18;20(1):284. Epub 2019 Dec 18.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
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http://dx.doi.org/10.1186/s13059-019-1899-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918601PMC
December 2019

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism.

Curr Biol 2019 09 12;29(18):3041-3052.e4. Epub 2019 Sep 12.

RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan. Electronic address:

Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.
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http://dx.doi.org/10.1016/j.cub.2019.07.086DOI Listing
September 2019

Durum wheat genome highlights past domestication signatures and future improvement targets.

Nat Genet 2019 05 8;51(5):885-895. Epub 2019 Apr 8.

CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.
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http://dx.doi.org/10.1038/s41588-019-0381-3DOI Listing
May 2019

Computational aspects underlying genome to phenome analysis in plants.

Plant J 2019 01;97(1):182-198

Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.

Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait-trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.
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http://dx.doi.org/10.1111/tpj.14179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849790PMC
January 2019

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

Authors:
Rudi Appels Kellye Eversole Catherine Feuillet Beat Keller Jane Rogers Nils Stein Curtis J Pozniak Nils Stein Frédéric Choulet Assaf Distelfeld Kellye Eversole Jesse Poland Jane Rogers Gil Ronen Andrew G Sharpe Curtis Pozniak Gil Ronen Nils Stein Omer Barad Kobi Baruch Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Andrew G Sharpe Gil Ben-Zvi Ambre-Aurore Josselin Nils Stein Martin Mascher Axel Himmelbach Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Jane Rogers François Balfourier Juan Gutierrez-Gonzalez Matthew Hayden Ambre-Aurore Josselin ChuShin Koh Gary Muehlbauer Raj K Pasam Etienne Paux Curtis J Pozniak Philippe Rigault Andrew G Sharpe Josquin Tibbits Vijay Tiwari Frédéric Choulet Gabriel Keeble-Gagnère Martin Mascher Ambre-Aurore Josselin Jane Rogers Manuel Spannagl Frédéric Choulet Daniel Lang Heidrun Gundlach Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Danara Ormanbekova Etienne Paux Verena Prade Hana Šimková Thomas Wicker Frédéric Choulet Manuel Spannagl David Swarbreck Hélène Rimbert Marius Felder Nicolas Guilhot Heidrun Gundlach Georg Haberer Gemy Kaithakottil Jens Keilwagen Daniel Lang Philippe Leroy Thomas Lux Klaus F X Mayer Sven Twardziok Luca Venturini Rudi Appels Hélène Rimbert Frédéric Choulet Angéla Juhász Gabriel Keeble-Gagnère Frédéric Choulet Manuel Spannagl Daniel Lang Michael Abrouk Georg Haberer Gabriel Keeble-Gagnère Klaus F X Mayer Thomas Wicker Frédéric Choulet Thomas Wicker Heidrun Gundlach Daniel Lang Manuel Spannagl Daniel Lang Manuel Spannagl Rudi Appels Iris Fischer Cristobal Uauy Philippa Borrill Ricardo H Ramirez-Gonzalez Rudi Appels Dominique Arnaud Smahane Chalabi Boulos Chalhoub Frédéric Choulet Aron Cory Raju Datla Mark W Davey Matthew Hayden John Jacobs Daniel Lang Stephen J Robinson Manuel Spannagl Burkhard Steuernagel Josquin Tibbits Vijay Tiwari Fred van Ex Brande B H Wulff Curtis J Pozniak Stephen J Robinson Andrew G Sharpe Aron Cory Moussa Benhamed Etienne Paux Abdelhafid Bendahmane Lorenzo Concia David Latrasse Jane Rogers John Jacobs Michael Alaux Rudi Appels Jan Bartoš Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Thomas Letellier Odd-Arne Olsen Hana Šimková Kuldeep Singh Miroslav Valárik Edwin van der Vossen Sonia Vautrin Song Weining Abraham Korol Zeev Frenkel Tzion Fahima Vladimir Glikson Dina Raats Jane Rogers Vijay Tiwari Bikram Gill Etienne Paux Jesse Poland Jaroslav Doležel Jarmila Číhalíková Hana Šimková Helena Toegelová Jan Vrána Pierre Sourdille Benoit Darrier Rudi Appels Manuel Spannagl Daniel Lang Iris Fischer Danara Ormanbekova Verena Prade Delfina Barabaschi Luigi Cattivelli Pilar Hernandez Sergio Galvez Hikmet Budak Burkhard Steuernagel Jonathan D G Jones Kamil Witek Brande B H Wulff Guotai Yu Ian Small Joanna Melonek Ruonan Zhou Angéla Juhász Tatiana Belova Rudi Appels Odd-Arne Olsen Kostya Kanyuka Robert King Kirby Nilsen Sean Walkowiak Curtis J Pozniak Richard Cuthbert Raju Datla Ron Knox Krysta Wiebe Daoquan Xiang Antje Rohde Timothy Golds Jaroslav Doležel Jana Čížková Josquin Tibbits Hikmet Budak Bala Ani Akpinar Sezgi Biyiklioglu Gary Muehlbauer Jesse Poland Liangliang Gao Juan Gutierrez-Gonzalez Amidou N'Daiye Jaroslav Doležel Hana Šimková Jarmila Číhalíková Marie Kubaláková Jan Šafář Jan Vrána Hélène Berges Arnaud Bellec Sonia Vautrin Michael Alaux Françoise Alfama Anne-Françoise Adam-Blondon Raphael Flores Claire Guerche Thomas Letellier Mikaël Loaec Hadi Quesneville Curtis J Pozniak Andrew G Sharpe Sean Walkowiak Hikmet Budak Janet Condie Jennifer Ens ChuShin Koh Ron Maclachlan Yifang Tan Thomas Wicker Frédéric Choulet Etienne Paux Adriana Alberti Jean-Marc Aury François Balfourier Valérie Barbe Arnaud Couloux Corinne Cruaud Karine Labadie Sophie Mangenot Patrick Wincker Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Kuldeep Singh Parveen Chhuneja Om Prakash Gupta Suruchi Jindal Parampreet Kaur Palvi Malik Priti Sharma Bharat Yadav Nagendra K Singh JitendraP Khurana Chanderkant Chaudhary Paramjit Khurana Vinod Kumar Ajay Mahato Saloni Mathur Amitha Sevanthi Naveen Sharma Ram Sewak Tomar Jane Rogers John Jacobs Michael Alaux Arnaud Bellec Hélène Berges Jaroslav Doležel Catherine Feuillet Zeev Frenkel Bikram Gill Abraham Korol Edwin van der Vossen Sonia Vautrin Bikram Gill Gaganpreet Kaur Mingcheng Luo Sunish Sehgal Jan Bartoš Kateřina Holušová Ondřej Plíhal Matthew D Clark Darren Heavens George Kettleborough Jon Wright Miroslav Valárik Michael Abrouk Barbora Balcárková Kateřina Holušová Yuqin Hu Mingcheng Luo Elena Salina Nikolai Ravin Konstantin Skryabin Alexey Beletsky Vitaly Kadnikov Andrey Mardanov Michail Nesterov Andrey Rakitin Ekaterina Sergeeva Hirokazu Handa Hiroyuki Kanamori Satoshi Katagiri Fuminori Kobayashi Shuhei Nasuda Tsuyoshi Tanaka Jianzhong Wu Rudi Appels Matthew Hayden Gabriel Keeble-Gagnère Philippe Rigault Josquin Tibbits Odd-Arne Olsen Tatiana Belova Federica Cattonaro Min Jiumeng Karl Kugler Klaus F X Mayer Matthias Pfeifer Simen Sandve Xu Xun Bujie Zhan Hana Šimková Michael Abrouk Jacqueline Batley Philipp E Bayer David Edwards Satomi Hayashi Helena Toegelová Zuzana Tulpová Paul Visendi Song Weining Licao Cui Xianghong Du Kewei Feng Xiaojun Nie Wei Tong Le Wang Philippa Borrill Heidrun Gundlach Sergio Galvez Gemy Kaithakottil Daniel Lang Thomas Lux Martin Mascher Danara Ormanbekova Verena Prade Ricardo H Ramirez-Gonzalez Manuel Spannagl Nils Stein Cristobal Uauy Luca Venturini Nils Stein Rudi Appels Kellye Eversole Jane Rogers Philippa Borrill Luigi Cattivelli Frédéric Choulet Pilar Hernandez Kostya Kanyuka Daniel Lang Martin Mascher Kirby Nilsen Etienne Paux Curtis J Pozniak Ricardo H Ramirez-Gonzalez Hana Šimková Ian Small Manuel Spannagl David Swarbreck Cristobal Uauy

Science 2018 08 16;361(6403). Epub 2018 Aug 16.

John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK.

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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http://dx.doi.org/10.1126/science.aar7191DOI Listing
August 2018

Impact of transposable elements on genome structure and evolution in bread wheat.

Genome Biol 2018 08 17;19(1):103. Epub 2018 Aug 17.

GDEC, INRA, UCA (Université Clermont Auvergne), Clermont-Ferrand, France.

Background: Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.

Results: The overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.

Conclusions: Even though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
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http://dx.doi.org/10.1186/s13059-018-1479-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097303PMC
August 2018

Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris.

Nat Commun 2018 06 28;9(1):2515. Epub 2018 Jun 28.

Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Biologibygget, Framstredet 39, Tromsø, 9037, Norway.

A parasitic lifestyle, where plants procure some or all of their nutrients from other living plants, has evolved independently in many dicotyledonous plant families and is a major threat for agriculture globally. Nevertheless, no genome sequence of a parasitic plant has been reported to date. Here we describe the genome sequence of the parasitic field dodder, Cuscuta campestris. The genome contains signatures of a fairly recent whole-genome duplication and lacks genes for pathways superfluous to a parasitic lifestyle. Specifically, genes needed for high photosynthetic activity are lost, explaining the low photosynthesis rates displayed by the parasite. Moreover, several genes involved in nutrient uptake processes from the soil are lost. On the other hand, evidence for horizontal gene transfer by way of genomic DNA integration from the parasite's hosts is found. We conclude that the parasitic lifestyle has left characteristic footprints in the C. campestris genome.
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http://dx.doi.org/10.1038/s41467-018-04344-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6023873PMC
June 2018

The repetitive landscape of the 5100 Mbp barley genome.

Mob DNA 2017 20;8:22. Epub 2017 Dec 20.

PGSB - Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.

Background: While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated.

Results: Here, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low copy numbers. We found that the barley genome is highly compartmentalized with different types of TEs occupying different chromosomal "niches", such as distal, interstitial, or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Furthermore, their presence in gene promoters is associated with decreased methylation levels.

Conclusions: Our data show that TEs are major determinants of overall chromosome structure. We hypothesize that many of the the various chromosomal distribution patterns are the result of TE families targeting specific niches, rather than them accumulating where they have the least deleterious effects.
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http://dx.doi.org/10.1186/s13100-017-0102-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738225PMC
December 2017

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Plant J 2018 02;93(3):515-533

Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany.

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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http://dx.doi.org/10.1111/tpj.13801DOI Listing
February 2018

The pseudogenes of barley.

Plant J 2018 02 7;93(3):502-514. Epub 2018 Jan 7.

Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.

Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.
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http://dx.doi.org/10.1111/tpj.13794DOI Listing
February 2018

Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

J Biotechnol 2017 Nov 8;261:37-45. Epub 2017 Jul 8.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany. Electronic address:

Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes. This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community.
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http://dx.doi.org/10.1016/j.jbiotec.2017.07.006DOI Listing
November 2017

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.

Science 2017 07;357(6346):93-97

School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.

Wheat ( spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer ( ssp. ). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in () genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.
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http://dx.doi.org/10.1126/science.aan0032DOI Listing
July 2017

From plant genomes to phenotypes.

J Biotechnol 2017 Nov 9;261:46-52. Epub 2017 Jun 9.

Forschungszentrum Jülich (FZJ), Institute of Bio- and Geosciences (IBG-2) Plant Sciences, Wilhelm-Johnen-Straße, 52425 Jülich, Germany. Electronic address:

Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis. Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.
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http://dx.doi.org/10.1016/j.jbiotec.2017.06.003DOI Listing
November 2017

A chromosome conformation capture ordered sequence of the barley genome.

Nature 2017 04;544(7651):427-433

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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http://dx.doi.org/10.1038/nature22043DOI Listing
April 2017

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Genome Res 2017 05;27(5):885-896

Earlham Institute, Norwich, NR4 7UZ, United Kingdom.

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
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http://dx.doi.org/10.1101/gr.217117.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411782PMC
May 2017

PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

Methods Mol Biol 2017 ;1533:33-44

Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.

Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.
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http://dx.doi.org/10.1007/978-1-4939-6658-5_2DOI Listing
January 2018

Towards a whole-genome sequence for rye (Secale cereale L.).

Plant J 2017 Mar 8;89(5):853-869. Epub 2017 Feb 8.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany.

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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http://dx.doi.org/10.1111/tpj.13436DOI Listing
March 2017

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

Nucleic Acids Res 2016 Jan 2;44(D1):D1141-7. Epub 2015 Nov 2.

Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany.

PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).
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http://dx.doi.org/10.1093/nar/gkv1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702821PMC
January 2016

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M.

PLoS Genet 2015 Oct 22;11(10):e1005588. Epub 2015 Oct 22.

Plant Systems Biology, Technische Universität München, Freising, Germany.

Plants integrate seasonal cues such as temperature and day length to optimally adjust their flowering time to the environment. Compared to the control of flowering before and after winter by the vernalization and day length pathways, mechanisms that delay or promote flowering during a transient cool or warm period, especially during spring, are less well understood. Due to global warming, understanding this ambient temperature pathway has gained increasing importance. In Arabidopsis thaliana, FLOWERING LOCUS M (FLM) is a critical flowering regulator of the ambient temperature pathway. FLM is alternatively spliced in a temperature-dependent manner and the two predominant splice variants, FLM-ß and FLM-δ, can repress and activate flowering in the genetic background of the A. thaliana reference accession Columbia-0. The relevance of this regulatory mechanism for the environmental adaptation across the entire range of the species is, however, unknown. Here, we identify insertion polymorphisms in the first intron of FLM as causative for accelerated flowering in many natural A. thaliana accessions, especially in cool (15°C) temperatures. We present evidence for a potential adaptive role of this structural variation and link it specifically to changes in the abundance of FLM-ß. Our results may allow predicting flowering in response to ambient temperatures in the Brassicaceae.
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http://dx.doi.org/10.1371/journal.pgen.1005588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619661PMC
October 2015

chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes.

BMC Plant Biol 2014 Dec 10;14:348. Epub 2014 Dec 10.

Background: Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner.

Description: We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering.

Conclusions: This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.
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http://dx.doi.org/10.1186/s12870-014-0348-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266971PMC
December 2014

Genes on B chromosomes: old questions revisited with new tools.

Biochim Biophys Acta 2015 Jan 3;1849(1):64-70. Epub 2014 Dec 3.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Stadt Seeland, Germany. Electronic address:

Background: B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Often, they have been considered as 'junk DNA' or genomic parasites without functional genes.

Scope Of Review: Due to recent advances in sequencing technologies, it became possible to investigate their DNA composition, transcriptional activity and effects on the host transcriptome profile in detail. Here, we review the most recent findings regarding the gene content of B chromosomes and their transcriptional activities and discuss these findings in the context of comparable biological phenomena, like sex chromosomes, aneuploidy and pseudogenes.

Major Conclusions: Recent data suggest that B chromosomes carry transcriptionally active genic sequences which could affect the transcriptome profile of their host genome.

General Significance: These findings are gradually changing our view that B chromosomes are solely genetically inert selfish elements without any functional genes. This at one side could partly explain the deleterious effects which are associated with their presence. On the other hand it makes B chromosome a nice model for studying regulatory mechanisms of duplicated genes and their evolutionary consequences.
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http://dx.doi.org/10.1016/j.bbagrm.2014.11.007DOI Listing
January 2015

Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton).

Genetics 2014 Aug 6;197(4):1153-63. Epub 2014 Jun 6.

Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Department of Plant Biology, University of Georgia, Athens, Georgia 30602 Department of Crop and Soil Science and Department of Genetics, University of Georgia, Athens, Georgia 30602

Genome duplication is thought to be central to the evolution of morphological complexity, and some polyploids enjoy a variety of capabilities that transgress those of their diploid progenitors. Comparison of genomic sequences from several tetraploid (AtDt) Gossypium species and genotypes with putative diploid A- and D-genome progenitor species revealed that unidirectional DNA exchanges between homeologous chromosomes were the predominant mechanism responsible for allelic differences between the Gossypium tetraploids and their diploid progenitors. Homeologous gene conversion events (HeGCEs) gradually subsided, declining to rates similar to random mutation during radiation of the polyploid into multiple clades and species. Despite occurring in a common nucleus, preservation of HeGCE is asymmetric in the two tetraploid subgenomes. At-to-Dt conversion is far more abundant than the reciprocal, is enriched in heterochromatin, is highly correlated with GC content and transposon distribution, and may silence abundant A-genome-derived retrotransposons. Dt-to-At conversion is abundant in euchromatin and genes, frequently reversing losses of gene function. The long-standing observation that the nonspinnable-fibered D-genome contributes to the superior yield and quality of tetraploid cotton fibers may be explained by accelerated Dt to At conversion during cotton domestication and improvement, increasing dosage of alleles from the spinnable-fibered A-genome. HeGCE may provide an alternative to (rare) reciprocal DNA exchanges between chromosomes in heterochromatin, where genes have approximately five times greater abundance of Dt-to-At conversion than does adjacent intergenic DNA. Spanning exon-to-gene-sized regions, HeGCE is a natural noninvasive means of gene transfer with the precision of transformation, potentially important in genetic improvement of many crop plants.
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http://dx.doi.org/10.1534/genetics.114.166124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125390PMC
August 2014

An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

BMC Genomics 2014 Apr 27;15:312. Epub 2014 Apr 27.

J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA.

Background: Medicago truncatula, a close relative of alfalfa, is a preeminent model for studying nitrogen fixation, symbiosis, and legume genomics. The Medicago sequencing project began in 2003 with the goal to decipher sequences originated from the euchromatic portion of the genome. The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011.

Results: Here we describe a further improved and refined version of the M. truncatula genome (Mt4.0) based on de novo whole genome shotgun assembly of a majority of Illumina and 454 reads using ALLPATHS-LG. The ALLPATHS-LG scaffolds were anchored onto the pseudomolecules on the basis of alignments to both the optical map and the genotyping-by-sequencing (GBS) map. The Mt4.0 pseudomolecules encompass ~360 Mb of actual sequences spanning 390 Mb of which ~330 Mb align perfectly with the optical map, presenting a drastic improvement over the BAC-based Mt3.5 which only contained 70% sequences (~250 Mb) of the current version. Most of the sequences and genes that previously resided on the unanchored portion of Mt3.5 have now been incorporated into the Mt4.0 pseudomolecules, with the exception of ~28 Mb of unplaced sequences. With regard to gene annotation, the genome has been re-annotated through our gene prediction pipeline, which integrates EST, RNA-seq, protein and gene prediction evidences. A total of 50,894 genes (31,661 high confidence and 19,233 low confidence) are included in Mt4.0 which overlapped with ~82% of the gene loci annotated in Mt3.5. Of the remaining genes, 14% of the Mt3.5 genes have been deprecated to an "unsupported" status and 4% are absent from the Mt4.0 predictions.

Conclusions: Mt4.0 and its associated resources, such as genome browsers, BLAST-able datasets and gene information pages, can be found on the JCVI Medicago web site (http://www.jcvi.org/medicago). The assembly and annotation has been deposited in GenBank (BioProject: PRJNA10791). The heavily curated chromosomal sequences and associated gene models of Medicago will serve as a better reference for legume biology and comparative genomics.
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http://dx.doi.org/10.1186/1471-2164-15-312DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234490PMC
April 2014

A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms.

Plant Physiol 2014 Jan 15;164(1):412-23. Epub 2013 Nov 15.

Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466 Stadt Seeland, Germany.

Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
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http://dx.doi.org/10.1104/pp.113.228213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875818PMC
January 2014

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.

Nature 2012 Dec;492(7429):423-7

Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.

Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
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http://dx.doi.org/10.1038/nature11798DOI Listing
December 2012

MIPS PlantsDB: a database framework for comparative plant genome research.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D1144-51. Epub 2012 Nov 29.

Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany.

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.
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http://dx.doi.org/10.1093/nar/gks1153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531202PMC
January 2013

Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences.

Proc Natl Acad Sci U S A 2012 Aug 30;109(33):13343-6. Epub 2012 Jul 30.

Institute of Bioinformatics and Systems Biology, German Research Center for Environmental Health, 85764 Neuherberg, Germany.

Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.
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http://dx.doi.org/10.1073/pnas.1204237109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421217PMC
August 2012