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

作者：Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata‐Otsubo, José 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 L. 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, Moaïne El Baidouri, Marie‐Christine Carpentier, Éric Lasserre, Richard Cooke, Daniel da Rosa Farias, Luciano Carlos da Maia, Railson Schreinert 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 J Henry, Yue-Ie Hsing, Nori Kurata, Antônio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware, Rod A. Wing · 发表于：Nature Genetics · 年份：2018 · DOI：10.1038/s41588-018-0040-0 · 被引用次数：638 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、Plant Disease Resistance and Genetics

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. Genome assemblies of 13 domesticated and wild rice relatives reveal salient features of genome evolution across the genus Oryza, especially rapid species diversification and turnover of transposons. This study also releases a complete long-read assembly of IR 8 ‘Miracle Rice’.