Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 111, Issue 46, Pages E4954-E4962Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1418307111
Keywords
comparative genomics; full-genome sequencing; genomic variation; positive selection; Oryza
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Funding
- Top Talents Program of Yunnan Province [20080A009]
- Hundreds Oversea Talents Program of Yunnan Province
- project of the Yunnan Innovation Team
- Natural Science Foundation of Yunnan Province [2010CC011]
- Hundreds Talents Program of the Chinese Academy of Sciences (CAS)
- CAS [KSCX2-YW-N-029]
- Chinese Department of Science and Technology (973 Program) [2007CB815703]
- Kunming Institute of Botany, CAS
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Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
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