Jianwei Zhanga,b,c,1, Ling-Ling Chena,1, Feng Xinga,1, David A. Kudrnab,c, Wen Yaoa, Dario Copettib,c,d, Ting Mua, Weiming Lia, Jia-Ming Songa, Weibo Xiea, Seunghee Leeb,c, Jayson Talagb,c, Lin Shaoa, Yue Ana, Chun-Liu Zhanga, Yidan Ouyanga, Shuai Suna, Wen-Biao Jiaoa, Fang Lva, Bogu Dua, Meizhong Luoa, Carlos Ernesto Maldonadob,c, Jose Luis Goicoecheab,c, Lizhong Xionga, Changyin Wua, Yongzhong Xinga, Dao-Xiu Zhoua, Sibin Yua, Yu Zhaoa, Gongwei Wanga, Yeisoo Yub,c,2, Yijie Luoa, Zhi-Wei Zhoua, Beatriz Elena Padilla Hurtadob,c, Ann Danowitzb, Rod A. Wingb,c,d,3, and Qifa Zhanga,3
Published online before print August 17, 2016, doi: 10.1073/pnas.1611012113
PNAS August 17, 2016
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.
Oryza sativa | reference genomes | BAC-by-BAC | strategy transcriptome
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