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

Authors

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

Nature Genetics (2018)
doi:10.1038/s41588-018-0040-0

Received: 29 October 2017
Accepted: 18 December 2017
Published online: 22 January 2018

https://www.nature.com/articles/s41588-018-0040-0

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.