Whole-Genome Sequencing of Oryza brachyantha Reveals Mechanisms Underlying Oryza Genome Evolution

The genus Oryza, including two cultivated rice and more than twenty wild rice species, is an ideal system for plant comparative, evolutionary and functional genomics studies. The wild rice species contains valuable gene resources for rice improvement. To facilitate the utilization of these wild resources, the International Oryza Map Alignment Project (I-OMAP) was organized by Prof. Rod Wing from University of Arizona in 2009 to construct a complete genome map of all of the Oryza species and to conduct researches in evolutionary and functional genomics.

 

In collaborations with BGI-Shenzhen and University of Arizona, Prof. Mingsheng Chen’ group at the Institute of Genetics and Developmental Biology, Chinese Academe of Sciences, generated 261 Mb genome sequence of O. brachyantha. The authors revealed that the compact genome of O. brachyantha resulted from recent silencing of LTR retrotransposons and massive internal deletions of ancient elements. Comparison with the rice genome indicated that many gene families were expanded in rice, where tandem duplication and gene movementmediated bydouble-strand break repair are responsible for the amplification of these genes.

 

The authors also observed that segmental and tandem duplications, further expanded by transposable element insertions, contributed to transition from euchromatin to heterochromatin in the rice genome, reflecting the dynamic nature of the Oryza genomes.

 

This work has been published online on March 12, 2013 in Nature Communications (link). Dr. Jinfeng Chen is the first author of this paper. This work was supported by grants from the National Natural Science Foundation of China and the State Key Laboratory of Plant Genomics.

 

AUTHOR CONTACT:

Mingsheng Chen, Ph.D.

Institute of Genetics and Developmetnal Biology, Chinese Academy of Sciences, Beijing, China.

E-mail: mschen@genetics.ac.cn

 

Figure 1. Alignment of 36 sequence blocks of O. brachyantha to rice chromosomes. Rice chromosomes are shown on the left, filled with density of repeat elements for every 100 kb window. Sequence blocks of O. brachyantha on each chromosome are represented by black boxes on the right.