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

• Published in: Proceedings of the National Academy of Sciences - PNAS 2016-08, Vol.113 (35), p.E5163-E5171
• Main Authors: Zhang, Jianwei, 张建伟, Chen, Ling-Ling, 陈玲玲, Xing, Feng, 邢锋, Kudrna, David A., Yao, Wen, 姚文, Copetti, Dario, Mu, Ting, 穆婷, Li, Weiming, 李伟明, Song, Jia-Ming, 宋佳明, Xie, Weibo, 谢为博, Lee, Seunghee, Talag, Jayson, Shao, Lin, 邵林, An, Yue, 安玥, Zhang, Chun-Liu, 张春柳, Ouyang, Yidan, 欧阳亦聃, Sun, Shuai, 孙帅, Jiao, Wen-Biao, 焦文标, Lv, Fang, 吕芳, Du, Bogu, 杜博贾, Luo, Meizhong, 罗美中, Maldonado, Carlos Ernesto, Goicoechea, Jose Luis, Xiong, Lizhong, 熊立仲, Wu, Changyin, 吴昌银, Xing, Yongzhong, 邢永忠, Zhou, Dao-Xiu, 周道绣, Yu, Sibin, 余四斌, Zhao, Yu, 赵毓, Wang, Gongwei, 王功伟, Yu, Yeisoo, Luo, Yijie, 罗艺洁, Zhou, Zhi-Wei, 周智伟, Hurtado, Beatriz Elena Padilla, Danowitz, Ann, Wing, Rod A., Zhang, Qifa, 张启发
• Format: Article
• Language: English
• Subjects: Biological Sciences; Gene expression; Genetic diversity; Genomes; Oryza sativa; Plant biology; PNAS Plus; Rice
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1611012113

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) andMinghui 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 non-transposable 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.