Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

Authors

Jinfeng Chen, Quanfei Huang, Dongying Gao, Junyi Wang, Yongshan Lang, Tieyan Liu, Bo Li, Zetao Bai, Jose Luis Goicoechea, Chengzhi Liang, Chengbin Chen, Wenli Zhang, Shouhong Sun, Yi Liao, Xuemei Zhang, Lu Yang, Chengli Song, Meijiao Wang, Jinfeng Shi

Geng Liu, Junjie Liu, Heling Zhou, Weili Zhou, Qiulin Yu, Na An, Yan Chen, Qingle Cai, Bo Wang, Binghang Liu, Jiumeng Min, Ying Huang, Honglong Wu, Zhenyu Li, Yong Zhang, Ye Yin, Wenqin Song, Jiming Jiang, Scott A. Jackson, Rod A. Wing, Jun Wang

Mingsheng Chen

Nature Communications 4, Article number: 1595 doi:10.1038/ncomms2596

Received 01 October 2012

Accepted 11 February 2013

Published 12 March 2013

Abstract

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

http://www.nature.com/ncomms/journal/v4/n3/full/ncomms2596.html