The Genomes of Oryza sativa: A History of Duplications

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 f...

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Main Authors:	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
Format:	Online
Language:	English
Published:	Public Library of Science 2005
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038/

id	pubmed-546038
recordtype	oai_dc
spelling	pubmed-5460382005-02-01 The Genomes of Oryza sativa: A History of Duplications 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 Research Article 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. Public Library of Science 2005-02 2005-02-01 /pmc/articles/PMC546038/ /pubmed/15685292 http://dx.doi.org/10.1371/journal.pbio.0030038 Text en Copyright: © 2005 Yu et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	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
spellingShingle	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 The Genomes of Oryza sativa: A History of Duplications
author_facet	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
author_sort	Yu, Jun
title	The Genomes of Oryza sativa: A History of Duplications
title_short	The Genomes of Oryza sativa: A History of Duplications
title_full	The Genomes of Oryza sativa: A History of Duplications
title_fullStr	The Genomes of Oryza sativa: A History of Duplications
title_full_unstemmed	The Genomes of Oryza sativa: A History of Duplications
title_sort	genomes of oryza sativa: a history of duplications
description	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.
publisher	Public Library of Science
publishDate	2005
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038/
_version_	1611370588486500352

The Genomes of Oryza sativa: A History of Duplications

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