title: Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Feng
authors.initials: F
authors.lastname: Xing
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: David A
authors.initials: DA
authors.lastname: Kudrna
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Ting
authors.initials: T
authors.lastname: Mu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Weiming
authors.initials: W
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Song
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Weibo
authors.identifier: 0000-0002-2768-3572
authors.initials: W
authors.lastname: Xie
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Seunghee
authors.initials: S
authors.lastname: Lee
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Jayson
authors.initials: J
authors.lastname: Talag
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Lin
authors.initials: L
authors.lastname: Shao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Yue
authors.initials: Y
authors.lastname: An
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Chun-Liu
authors.initials: CL
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Yidan
authors.initials: Y
authors.lastname: Ouyang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Shuai
authors.initials: S
authors.lastname: Sun
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Wen-Biao
authors.initials: WB
authors.lastname: Jiao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Fang
authors.initials: F
authors.lastname: Lv
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Bogu
authors.initials: B
authors.lastname: Du
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Meizhong
authors.initials: M
authors.lastname: Luo
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Carlos Ernesto
authors.initials: CE
authors.lastname: Maldonado
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Changyin
authors.initials: C
authors.lastname: Wu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Xing
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Dao-Xiu
authors.initials: DX
authors.lastname: Zhou
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Yijie
authors.initials: Y
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
authors.forename: Zhi-Wei
authors.initials: ZW
authors.lastname: Zhou
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Beatriz Elena Padilla
authors.initials: BE
authors.lastname: Hurtado
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721;
authors.forename: Ann
authors.initials: A
authors.lastname: Danowitz
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721; International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines qifazh@mail.hzau.edu.cn rwing@mail.arizona.edu.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; qifazh@mail.hzau.edu.cn rwing@mail.arizona.edu.
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D054643:INDEL Mutation; D012275:Oryza / Q000145:classification / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity
keywords: BAC-by-BAC strategy; Oryza sativa; reference genomes; transcriptome