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