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 Dave
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 S.B.
Zhao Yu
Wang Gongwei
Yu Yeisoo
Luo Yijie
Zhou Zhi-Wei
Hurtado Beatriz Elena Padilla
Danowitz Ann
Wing Rod A.
Zhang Qifa
· 2016
期刊名称：
Proceedings of the National Academy of Sciences of the United States of America
2016 年
113 卷
35 期
摘要：
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.
会员登录
