Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Jianwei - Zhang, Ling Ling Chen, Feng Xing, David A Kudrna, Wen Yao, Dario Copetti, Ting Mu, Weiming Li, Jia Ming Song, Weibo Xie, Seunghee Lee, Jayson Talag, Lin Shao, Yue An, Chun Liu Zhang, Yidan Ouyang, Shuai Sun, Wen Biao Jiao, Fang Lv, Bogu DuMeizhong Luo, Carlos Ernesto Maldonado, Jose Luis Goicoechea, Lizhong Xiong, Changyin Wu, Yongzhong Xing, Dao Xiu Zhou, Sibin Yu, Yu Zhao, Gongwei Wang, Yeisoo Yu, Yijie Luo, Zhi Wei Zhou, Beatriz Elena Padilla Hurtado, Ann Danowitz, Rod A Wing, Qifa Zhang

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63(MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

Original languageEnglish (US)
Pages (from-to)E5163-E5171
JournalProceedings of the National Academy of Sciences of the United States of America
Volume113
Issue number35
DOIs
StatePublished - Aug 30 2016

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Genome
Genomic Segmental Duplications
Genes
Genome Size
Oryza
Gene Expression Profiling

Keywords

  • Bac-by-bac strategy
  • Oryza sativa
  • Reference genomes
  • Transcriptome

ASJC Scopus subject areas

  • General

Cite this

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. / Zhang, Jianwei -; Chen, Ling Ling; Xing, Feng; Kudrna, David A; Yao, Wen; Copetti, Dario; Mu, Ting; Li, Weiming; Song, Jia Ming; Xie, Weibo; Lee, Seunghee; Talag, Jayson; Shao, Lin; An, Yue; Zhang, Chun Liu; Ouyang, Yidan; Sun, Shuai; Jiao, Wen Biao; Lv, Fang; Du, Bogu; Luo, Meizhong; Maldonado, Carlos Ernesto; Goicoechea, Jose Luis; Xiong, Lizhong; Wu, Changyin; Xing, Yongzhong; Zhou, Dao Xiu; Yu, Sibin; Zhao, Yu; Wang, Gongwei; Yu, Yeisoo; Luo, Yijie; Zhou, Zhi Wei; Hurtado, Beatriz Elena Padilla; Danowitz, Ann; Wing, Rod A; Zhang, Qifa.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, No. 35, 30.08.2016, p. E5163-E5171.

Research output: Contribution to journalArticle

Zhang, J, Chen, LL, Xing, F, Kudrna, DA, Yao, W, Copetti, D, Mu, T, Li, W, Song, JM, Xie, W, Lee, S, Talag, J, Shao, L, An, Y, Zhang, CL, Ouyang, Y, Sun, S, Jiao, WB, Lv, F, Du, B, Luo, M, Maldonado, CE, Goicoechea, JL, Xiong, L, Wu, C, Xing, Y, Zhou, DX, Yu, S, Zhao, Y, Wang, G, Yu, Y, Luo, Y, Zhou, ZW, Hurtado, BEP, Danowitz, A, Wing, RA & Zhang, Q 2016, 'Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 35, pp. E5163-E5171. https://doi.org/10.1073/pnas.1611012113
Zhang, Jianwei - ; Chen, Ling Ling ; Xing, Feng ; Kudrna, David A ; Yao, Wen ; Copetti, Dario ; Mu, Ting ; Li, Weiming ; Song, Jia Ming ; Xie, Weibo ; Lee, Seunghee ; Talag, Jayson ; Shao, Lin ; An, Yue ; Zhang, Chun Liu ; Ouyang, Yidan ; Sun, Shuai ; Jiao, Wen Biao ; Lv, Fang ; Du, Bogu ; Luo, Meizhong ; Maldonado, Carlos Ernesto ; Goicoechea, Jose Luis ; Xiong, Lizhong ; Wu, Changyin ; Xing, Yongzhong ; Zhou, Dao Xiu ; Yu, Sibin ; Zhao, Yu ; Wang, Gongwei ; Yu, Yeisoo ; Luo, Yijie ; Zhou, Zhi Wei ; Hurtado, Beatriz Elena Padilla ; Danowitz, Ann ; Wing, Rod A ; Zhang, Qifa. / Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. In: Proceedings of the National Academy of Sciences of the United States of America. 2016 ; Vol. 113, No. 35. pp. E5163-E5171.
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AU - Zhang, Jianwei -

AU - Chen, Ling Ling

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AU - Kudrna, David A

AU - Yao, Wen

AU - Copetti, Dario

AU - Mu, Ting

AU - Li, Weiming

AU - Song, Jia Ming

AU - Xie, Weibo

AU - Lee, Seunghee

AU - Talag, Jayson

AU - Shao, Lin

AU - An, Yue

AU - Zhang, Chun Liu

AU - Ouyang, Yidan

AU - Sun, Shuai

AU - Jiao, Wen Biao

AU - Lv, Fang

AU - Du, Bogu

AU - Luo, Meizhong

AU - Maldonado, Carlos Ernesto

AU - Goicoechea, Jose Luis

AU - Xiong, Lizhong

AU - Wu, Changyin

AU - Xing, Yongzhong

AU - Zhou, Dao Xiu

AU - Yu, Sibin

AU - Zhao, Yu

AU - Wang, Gongwei

AU - Yu, Yeisoo

AU - Luo, Yijie

AU - Zhou, Zhi Wei

AU - Hurtado, Beatriz Elena Padilla

AU - Danowitz, Ann

AU - Wing, Rod A

AU - Zhang, Qifa

PY - 2016/8/30

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N2 - Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63(MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

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KW - Bac-by-bac strategy

KW - Oryza sativa

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KW - Transcriptome

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