Multiple wheat genomes reveal global variation in modern breeding.
Sean Walkowiak,Sean Walkowiak,Liangliang Gao,Cécile 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 T. Nilsen,Catharine Aquino,Axel Himmelbach,Dario Copetti,Dario Copetti,Tomohiro Ban,Luca Venturini,Michael W. Bevan,Bernardo J. 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 J. Gutierrez-Gonzalez,Gwyneth Halstead-Nussloch,Masaomi Hatakeyama,Chu Shin Koh,Jasline Deek,Alejandro C. Costamagna,Pierre R. Fobert,Darren Heavens,Hiroyuki Kanamori,Kanako Kawaura,Fuminori Kobayashi,Ksenia V. Krasileva,Tony Kuo,Tony Kuo,Neil McKenzie,Kazuki Murata,Yusuke Nabeka,Timothy Paape,Sudharsan Padmarasu,Lawrence Percival-Alwyn,Sateesh Kagale,Uwe Scholz,Jun Sese,Philomin Juliana,Ravi P. Singh,Rie Shimizu-Inatsugi,David Swarbreck,James Cockram,Hikmet Budak,Toshiaki Tameshige,Tsuyoshi Tanaka,Hiroyuki Tsuji,Jonathan M. Wright,Jianzhong Wu,Burkhard Steuernagel,Ian Small,Sylvie Cloutier,Gabriel Keeble-Gagnère,Gary J. Muehlbauer,Josquin Tibbets,Shuhei Nasuda,Joanna Melonek,Pierre Hucl,Andrew G. Sharpe,Matthew D. Clark,Erik Legg,Arvind K. Bharti,Peter Langridge,Anthony Hall,Cristobal Uauy,Martin Mascher,Simon G. Krattinger,Simon G. Krattinger,Hirokazu Handa,Kentaro Shimizu,Kentaro Shimizu,Assaf Distelfeld,Kenneth J. Chalmers,Beat Keller,Klaus F. X. Mayer,Jesse Poland,Nils Stein,Nils Stein,Curt A. McCartney,Manuel Spannagl,Thomas Wicker,Curtis J. Pozniak +103 more
TLDR
Comparative analysis of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.Abstract:
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 genome1, and the lack of genome-assembly data for multiple wheat lines2,3. 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 stresses4,5. 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 Sm16, 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.read more
Citations
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Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Peng Qin,Hongwei Lu,Huilong Du,Hao Wang,Weilan Chen,Zhuo Chen,Qiang He,Shujun Ou,Hongyu Zhang,Xuanzhao Li,Xiuxiu Li,Yan Li,Yi Liao,Qiang Gao,Bin Tu,Hua Yuan,Bingtian Ma,Yuping Wang,Yangwen Qian,Shijun Fan,Weitao Li,Jing Wang,Min He,Junjie Yin,Ting Li,Ning Jiang,Xuewei Chen,Chengzhi Liang,Shigui Li +28 more
TL;DR: In this paper, a pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations, were developed to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
Journal ArticleDOI
Long-read sequence assembly: a technical evaluation in barley
Martin Mascher,Thomas Wicker,Jerry Jenkins,Christopher Plott,Thomas Lux,Chu Shin Koh,Jennifer Ens,Heidrun Gundlach,Lori Beth Boston,Zuzana Tulpová,Samuel Holden,Inmaculada Hernández-Pinzón,Uwe Scholz,Klaus F. X. Mayer,Manuel Spannagl,Curtis J. Pozniak,Andrew G. Sharpe,Hana Šimková,Matthew J. Moscou,Jane Grimwood,Jeremy Schmutz,Nils Stein,Nils Stein +22 more
TL;DR: In this article, the authors compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare).
Journal ArticleDOI
WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat.
Shengwei Ma,Shengwei Ma,Meng Wang,Jianhui Wu,Weilong Guo,Yongming Chen,Guangwei Li,Yanpeng Wang,Weiming Shi,Guangmin Xia,Daolin Fu,Zhensheng Kang,Fei Ni +12 more
Journal ArticleDOI
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
Andrew D. Yates,James E. Allen,Ridwan M Amode,Andrey G Azov,Matthieu Barba,Andrés Becerra,Jyothish Bhai,Lahcen I. Campbell,Manuel Carbajo Martinez,Marc Chakiachvili,Kapeel Chougule,Mikkel B. Christensen,Bruno Contreras-Moreira,Alayne Cuzick,Luca Da Rin Fioretto,Paul Davis,Nishadi De Silva,Stavros Diamantakis,Sarah Dyer,Justin Elser,Carla Valeria Filippi,Carla Valeria Filippi,Carla Valeria Filippi,Astrid Gall,Dionysios Grigoriadis,Cristina Guijarro-Clarke,Parul Gupta,Kim E. Hammond-Kosack,Kevin L. Howe,Pankaj Jaiswal,Vinay Kaikala,Vivek Kumar,Sunita Kumari,Nick Langridge,Tuan Le,Manuel Luypaert,Gareth Maslen,Thomas Maurel,Benjamin Moore,Matthieu Muffato,Aleena Mushtaq,Guy Naamati,Sushma Naithani,Andrew Olson,Anne Parker,Michael Paulini,Helder Pedro,Emily Perry,Justin Preece,Mark Quinton-Tulloch,Faye H. Rodgers,Marc Rosello,Magali Ruffier,James Seager,Vasily Sitnik,Michal Szpak,John Tate,Marcela K. Tello-Ruiz,Stephen J. Trevanion,Martin Urban,Doreen Ware,Doreen Ware,Sharon Wei,Gary Williams,Andrea Winterbottom,Magdalena Zarowiecki,Robert D. Finn,Paul Flicek +67 more
TL;DR: Ensembl Genomes as discussed by the authors provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensemblgenomes.org).
Journal ArticleDOI
Two gap-free reference genomes and a global view of the centromere architecture in rice.
Jiaming Song,Jiaming Song,Wen-Zhao Xie,Shuo Wang,Yi-Xiong Guo,Dal-Hoe Koo,Dave Kudrna,Chenbo Gong,Yicheng Huang,Jia-Wu Feng,Wenhui Zhang,Yong Zhou,Andrea Zuccolo,Evan Long,Seunghee Lee,Jayson Talag,Run Zhou,Xi-Tong Zhu,Daojun Yuan,Joshua A. Udall,Weibo Xie,Rod A. Wing,Qifa Zhang,Jesse Poland,Jianwei Zhang,Ling-Ling Chen,Ling-Ling Chen +26 more
TL;DR: In this article, the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, were reported.
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