Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
- Stein, J. C.
- Yu, Y.
- Copetti, D.
- Zwickl, D. J.
- Zhang, L.
- Zhang, C.
- Chougule, K.
- Gao, D.
- Iwata, A.
- Goicoechea, J. L.
- Wei, S.
- Wang, J.
- Liao, Y.
- Wang, M.
- Jacquemin, J.
- Becker, C.
- Kudrna, D.
- Zhang, J.
- Londono, C. E. M.
- Song, X.
- Lee, S.
- Sanchez, P.
- Zuccolo, A.
- Ammiraju, J. S. S.
- Talag, J.
- Danowitz, A.
- Rivera, L. F.
- Gschwend, A. R.
- Noutsos, C.
- Wu, C. C.
- Kao, S. M.
- Zeng, J. W.
- Wei, F. J.
- Zhao, Q.
- Feng, Q.
- El Baidouri, M.
- Carpentier, M. C.
- Lasserre, E.
- Cooke, R.
- Rosa Farias, D. D.
- da Maia, L. C.
- Dos Santos, R. S.
- Nyberg, K. G.
- McNally, K. L.
- Mauleon, R.
- Alexandrov, N.
- Schmutz, J.
- Flowers, D.
- Fan, C.
- Weigel, D.
- Jena, K. K.
- Wicker, T.
- Chen, M.
- Han, B.
- Henry, R.
- Hsing, Y. C.
- Kurata, N.
- de Oliveira, A. C.
- Panaud, O.
- Jackson, S. A.
- Machado, C. A.
- Sanderson, M. J.
- Long, M.
- Ware, D.
- Wing, R. A.
DOIAbstract
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...
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