Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Joshua C. Stein; Yeisoo Yu; Dario Copetti; Derrick J. Zwickl; Li Zhang; Chengjun Zhang; Kapeel Chougule; Dongying Gao; Aiko Iwata; Jose Luis Goicoechea; Sharon Wei; Jun Wang; Yi Liao; Muhua Wang; Julie Jacquemin; Claude Becker; Dave Kudrna; Jianwei Zhang; Carlos E. M. Londono; Xiang Song; Seunghee Lee; Paul Sanchez; Andrea Zuccolo; Jetty S. S. Ammiraju; Jayson Talag; Ann Danowitz; Luis F. Rivera; Andrea R. Gschwend; Christos Noutsos; Cheng-chieh Wu; Shu-min Kao; Jhih-wun Zeng; Fu-jin Wei; Qiang Zhao; Qi Feng; Moaine El Baidouri; Marie-Christine Carpentier; Eric Lasserre; Richard Cooke; Daniel da Rosa Farias; Luciano Carlos da Maia; Railson S. dos Santos; Kevin G. Nyberg; Kenneth L. McNally; Ramil Mauleon; Nickolai Alexandrov; Jeremy Schmutz; Dave Flowers; Chuanzhu Fan; Detlef Weigel; Kshirod K. Jena; Thomas Wicker; Mingsheng Chen; Bin Han; Robert Henry; Yue-ie C. Hsing; Nori Kurata; Antonio Costa de Oliveira; Olivier Panaud; Scott A. Jackson; Carlos A. Machado; Michael J. Sanderson; Manyuan Long; Doreen Ware; Rod A. Wing; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

doi:10.1038/s41588-018-0040-0

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Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

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Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, …

Nature genetics, Vol.50(2), pp.285-296

01/02/2018

DOI: https://doi.org/10.1038/s41588-018-0040-0

PMID: 29358651

Abstract

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

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Title: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Creators - without role: Joshua C. Stein - Cold Spring Harbor Laboratory
Yeisoo Yu - University of Arizona
Dario Copetti - University of Arizona
Derrick J. Zwickl - University of Arizona
Li Zhang - University of Chicago
Chengjun Zhang - University of Chicago
Kapeel Chougule - University of Arizona
Dongying Gao - Applied Genetic Technologies
Aiko Iwata - Univ Georgia, Ctr Appl Genet Technol, Athens, GA 30602 USA
Jose Luis Goicoechea - University of Arizona
Sharon Wei - Cold Spring Harbor Laboratory
Jun Wang - Wayne State University
Yi Liao - State Key Laboratory of Plant Genomics
Muhua Wang - University of Arizona
Julie Jacquemin - University of Arizona
Claude Becker - Max Planck Institute for Developmental Biology
Dave Kudrna - University of Arizona
Jianwei Zhang - University of Arizona
Carlos E. M. Londono - University of Arizona
Xiang Song - University of Arizona
Seunghee Lee - University of Arizona
Paul Sanchez - University of Arizona
Andrea Zuccolo - University of Arizona
Jetty S. S. Ammiraju - University of Arizona
Jayson Talag - University of Arizona
Ann Danowitz - University of Arizona
Luis F. Rivera - University of Arizona
Andrea R. Gschwend - University of Chicago
Christos Noutsos - Cold Spring Harbor Laboratory
Cheng-chieh Wu - Institute of Plant and Microbial Biology, Academia Sinica
Shu-min Kao - Institute of Plant and Microbial Biology, Academia Sinica
Jhih-wun Zeng - Institute of Plant and Microbial Biology, Academia Sinica
Fu-jin Wei - Institute of Plant and Microbial Biology, Academia Sinica
Qiang Zhao - National Center for Gene Research
Qi Feng - National Center for Gene Research
Moaine El Baidouri - University of Perpignan
Marie-Christine Carpentier - University of Perpignan
Eric Lasserre - University of Perpignan
Richard Cooke - University of Perpignan
Daniel da Rosa Farias - Univ Fed Pelotas, Plant Genom & Breeding Ctr, Pelotas, Brazil
Luciano Carlos da Maia - Universidade Federal de Pelotas
Railson S. dos Santos - Universidade Federal de Pelotas
Kevin G. Nyberg - University of Maryland, College Park
Kenneth L. McNally - International Rice Research Institute
Ramil Mauleon - International Rice Research Institute
Nickolai Alexandrov - International Rice Research Institute
Jeremy Schmutz - HudsonAlpha Institute for Biotechnology
Dave Flowers - HudsonAlpha Institute for Biotechnology
Chuanzhu Fan - Wayne State University
Detlef Weigel - Max Planck Institute for Developmental Biology
Kshirod K. Jena - International Rice Research Institute
Thomas Wicker - University of Zurich
Mingsheng Chen - State Key Laboratory of Plant Genomics
Bin Han - National Center for Gene Research
Robert Henry - Agriculture and Food
Yue-ie C. Hsing - Institute of Plant and Microbial Biology, Academia Sinica
Nori Kurata - National Institute of Genetics
Antonio Costa de Oliveira - Universidade Federal de Pelotas
Olivier Panaud - Plant Genome and Development Laboratory
Scott A. Jackson - Applied Genetic Technologies
Carlos A. Machado - University of Maryland, College Park
Michael J. Sanderson - University of Arizona
Manyuan Long - University of Chicago
Doreen Ware - Cold Spring Harbor Laboratory
Rod A. Wing - University of Arizona
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Publication Details: Nature genetics, Vol.50(2), pp.285-296
Publisher: NATURE PORTFOLIO
Number of pages: 16
Grant note: 1127112 / Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) Alexander von Humboldt Research Award; Alexander von Humboldt Foundation CNPq; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) SFB 1101 / DFG; German Research Foundation (DFG) University of Perpignan BQR grant 1907-21000-030-00D / USDA-ARS; United States Department of Agriculture (USDA); USDA Agricultural Research Service AXA Chair in Genome Biology and Evolutionary Genomics; AXA Research Fund Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences 0321678; 0638541; 0822284; 1026200; 1127112 / US National Science Foundation; National Science Foundation (NSF)
Identifiers: 9942074208331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article