Journal Article

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

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

2018

Overview

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’.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 45 / 45/23 / 631/208/212 / 631/449/2491 / Agriculture / Animal Genetics and Genomics / BASIC BIOLOGICAL SCIENCES / Binding sites / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Chromosome rearrangements / Chromosomes / Cloning / Conserved Sequence / Crop diseases / Crops, Agricultural - genetics / Disease resistance / Domestication / Evolution / Evolution, Molecular / Famine / Famines / Gene Function / Genes / Genetic aspects / Genetic research / Genetic Speciation / Genetic Variation / Genetics / Genome, Plant / Genomes / Genomics / Green revolution / Haplotypes / Human Genetics / Innovations / Life Sciences / Molecular evolution / Mutation / Novels / Oryza / Oryza - classification / Oryza - genetics / Phylogeny / Plant diseases / Plant protection / Prevalence studies (Epidemiology) / Proteins / Rice / Species / Transposons / Trees