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Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set^[W],[OA]

^a Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721
^b State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
^c Department of Agronomy, Purdue University, West Lafayette, Indiana 47907-2054
^d Department of Horticulture, Michigan State University, East Lansing, Michigan 48823
^e Department of Genetics, University of Georgia, Athens, Georgia 30602-7223

² Address correspondence to rwing{at}ag.arizona.edu, sjackson{at}purdue.edu, or mschen{at}genetics.ac.cn

Oryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past 15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.

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Dynamic Evolution of Oryza Genomes

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