TY - JOUR
T1 - Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63
AU - Zhang, Jianwei
AU - Chen, Ling Ling
AU - Xing, Feng
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
N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20
PY - 2016/8/30
Y1 - 2016/8/30
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.
AB - 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.
UR - http://www.pnas.org/lookup/doi/10.1073/pnas.1611012113
UR - http://www.scopus.com/inward/record.url?scp=84984714310&partnerID=8YFLogxK
U2 - 10.1073/pnas.1611012113
DO - 10.1073/pnas.1611012113
M3 - Article
SN - 1091-6490
VL - 113
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 35
ER -