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The Genomes of Oryza sativa: A History of Duplications

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Author(s): Yu Jun | Wang Jun | Lin Wei | Li Songgang | Li Heng | Zhou Jun | Ni Peixiang | Dong Wei | Hu Songnian | Zeng Changqing | Zhang Jianguo | Zhang Yong | Li Ruiqiang | Xu Zuyuan | Li Shengting | Li Xianran | Zheng Hongkun | Cong Lijuan | Lin Liang | Yin Jianning | Geng Jianing | Li Guangyuan | Shi Jianping | Liu Juan | Lv Hong | Li Jun | Wang Jing | Deng Yajun | Ran Longhua | Shi Xiaoli | Wang Xiyin | Wu Qingfa | Li Changfeng | Ren Xiaoyu | Wang Jingqiang | Wang Xiaoling | Li Dawei | Liu Dongyuan | Zhang Xiaowei | Ji Zhendong | Zhao Wenming | Sun Yongqiao | Zhang Zhenpeng | Bao Jingyue | Han Yujun | Dong Lingli | Ji Jia | Chen Peng | Wu Shuming | Liu Jinsong | Xiao Ying | Bu Dongbo | Tan Jianlong | Yang Li | Ye Chen | Zhang Jingfen | Xu Jingyi | Zhou Yan | Yu Yingpu | Zhang Bing | Zhuang Shulin | Wei Haibin | Liu Bin | Lei Meng | Yu Hong | Li Yuanzhe | Xu Hao | Wei Shulin | He Ximiao | Fang Lijun | Zhang Zengjin | Zhang Yunze | Huang Xiangang | Su Zhixi | Tong Wei | Li Jinhong | Tong Zongzhong | Li Shuangli | Ye Jia | Wang Lishun | Fang Lin | Lei Tingting | Chen Chen | Chen Huan | Xu Zhao | Li Haihong | Huang Haiyan | Zhang Feng | Xu Huayong | Li Na | Zhao Caifeng | Li Shuting | Dong Lijun | Huang Yanqing | Li Long | Xi Yan | Qi Qiuhui | Li Wenjie | Zhang Bo | Hu Wei | Zhang Yanling | Tian Xiangjun | Jiao Yongzhi | Liang Xiaohu | Jin Jiao | Gao Lei | Zheng Weimou | Hao Bailin | Liu Siqi | Wang Wen | Yuan Longping | Cao Mengliang | McDermott Jason | Samudrala Ram | Wang Jian | Wong Gane Ka-Shu | Yang Huanming

Journal: PLoS Biology
ISSN 1544-9173

Volume: 3;
Issue: 2;
Date: 2005;
Original page

Keywords: Bioinformatics/Computational Biology | Evolution | Genetics/Genomics/Gene Therapy | Plant Science

ABSTRACT
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Tango Jona
Tangokurs Rapperswil-Jona

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