Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set

Jetty S.S. Ammiraju, Fei Lu, Abhijit Sanyal, Yeisoo Yu, Xiang Song, Ning Jiang, Ana Clara Pontaroli, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, Jinfeng Chen, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, Rod A. Wing

Research output: Contribution to journalArticle

86 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3191-3209
Number of pages19
JournalPlant Cell
Volume20
Issue number12
DOIs
StatePublished - Dec 2008

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology

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    Ammiraju, J. S. S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M., Jackson, S., & Wing, R. A. (2008). Dynamic evolution of Oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell, 20(12), 3191-3209. https://doi.org/10.1105/tpc.108.063727