TY - JOUR
T1 - Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
AU - Stein, Joshua C.
AU - Yu, Yeisoo
AU - Copetti, Dario
AU - Zwickl, Derrick J.
AU - Zhang, Li
AU - Zhang, Chengjun
AU - Chougule, Kapeel
AU - Gao, Dongying
AU - Iwata, Aiko
AU - Goicoechea, Jose Luis
AU - Wei, Sharon
AU - Wang, Jun
AU - Liao, Yi
AU - Wang, Muhua
AU - Jacquemin, Julie
AU - Becker, Claude
AU - Kudrna, Dave
AU - Zhang, Jianwei
AU - Londono, Carlos E.M.
AU - Song, Xiang
AU - Lee, Seunghee
AU - Sanchez, Paul
AU - Zuccolo, Andrea
AU - Ammiraju, Jetty S.S.
AU - Talag, Jayson
AU - Danowitz, Ann
AU - Rivera, Luis F.
AU - Gschwend, Andrea R.
AU - Noutsos, Christos
AU - Wu, Cheng Chieh
AU - Kao, Shu Min
AU - Zeng, Jhih Wun
AU - Wei, Fu Jin
AU - Zhao, Qiang
AU - Feng, Qi
AU - El Baidouri, Moaine
AU - Carpentier, Marie Christine
AU - Lasserre, Eric
AU - Cooke, Richard
AU - Rosa Farias, Daniel Da
AU - Da Maia, Luciano Carlos
AU - Dos Santos, Railson S.
AU - Nyberg, Kevin G.
AU - McNally, Kenneth L.
AU - Mauleon, Ramil
AU - Alexandrov, Nickolai
AU - Schmutz, Jeremy
AU - Flowers, Dave
AU - Fan, Chuanzhu
AU - Weigel, Detlef
AU - Jena, Kshirod K.
AU - Wicker, Thomas
AU - Chen, Mingsheng
AU - Han, Bin
AU - Henry, Robert
AU - Hsing, Yue Ie C.
AU - Kurata, Nori
AU - De Oliveira, Antonio Costa
AU - Panaud, Olivier
AU - Jackson, Scott A.
AU - Machado, Carlos A.
AU - Sanderson, Michael J.
AU - Long, Manyuan
AU - Ware, Doreen
AU - Wing, Rod A.
N1 - Funding Information:
We gratefully acknowledge CyVerse and the Texas Advanced Computing Center (TACC) for consultation and provision of computational resources. This material is based on work supported by the US National Science Foundation under grants 0321678, 0638541, 0822284 and 1026200 to S.A.J., C.A.M., M.J.S., M.L., D. Ware and R.A.W., the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, the Alexander von Humboldt Research Award and the AXA Chair in Genome Biology and Evolutionary Genomics to R.A.W., DFG SFB 1101 to C.B. and D. Weigel, a University of Perpignan BQR grant to M.-C.C., E.L. and O.P., a Senior Chair from Institut Universitaire de France to O.P. and a CNPq grant to A.C.d.O. D. Ware was also funded by US National Science Foundation grant 1127112 and USDA–ARS 1907-21000-030-00D. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the US National Science Foundation.
Funding Information:
We gratefully acknowledge CyVerse and the Texas Advanced Computing Center (TACC) for consultation and provision of computational resources. This material is based on work supported by the US National Science Foundation under grants 0321678, 0638541, 0822284 and 1026200 to S.A.J., C.A.M., M.J.S., M.L., D. Ware and R.A.W., the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, the Alexander von Humboldt Research Award and the AXA Chair in Genome Biology and Evolutionary Genomics to R.A.W., DFG SFB 1101 to C.B. and D. Weigel, a University of Perpignan BQR grant to M.-C.C., E.L. and O.P., a Senior Chair from Institut Universitaire de France to O.P. and a CNPq grant to A.C.d.O. D. Ware was also funded by US National Science Foundation grant 1127112 and USDA-ARS 1907-21000-030-00D.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/2/1
Y1 - 2018/2/1
N2 - 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.
AB - 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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U2 - 10.1038/s41588-018-0040-0
DO - 10.1038/s41588-018-0040-0
M3 - Article
C2 - 29358651
AN - SCOPUS:85040791254
SN - 1061-4036
VL - 50
SP - 285
EP - 296
JO - Nature Genetics
JF - Nature Genetics
IS - 2
ER -