ArticleProceedings of the National Academy of Sciences of the United States of America2016
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers, 1 of them a synthesis that pooled it.
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127 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.Journal of proteome research · 2024Pooled it
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- Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.Nucleic acids research · 2026Article
- Structural Variations Contribute to Subspeciation and Yield Heterosis in Rice.Plant biotechnology journal · 2025Article
- A novel method for effectively selecting fragments not associated with restriction sites for whole-genome genotyping.BMC biology · 2025Article
- Haplotype-resolved, gap-free genome assemblies provide insights into the divergence between Asian and European pears.Nature genetics · 2025Article
- A telomere-to-telomere gap-free assembly integrating multi-omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate.Plant biotechnology journal · 2025Article
- The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.BMC biology · 2025Article
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- Comprehensive characterization and diversity analysis of the HIS1 gene family in rice subpopulations for herbicide resistance.BMC plant biology · 2025Article
- Transcriptome Analysis of the Seed Shattering Mechanism inPlants (Basel, Switzerland) · 2024Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- The genetic basis and process of inbreeding depression in an elite hybrid rice.Science China. Life sciences · 2024Article
- Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms.Breeding science · 2024Article
- Characterization of Genomic, Physiological, and Probiotic Features ofFoods (Basel, Switzerland) · 2024Article
- A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence.Frontiers in plant science · 2024Article
- Dynamic patterns of gene expressional and regulatory variations in cotton heterosis.Frontiers in plant science · 2024Article
- A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.bioRxiv : the preprint server for biology · 2023Article
- A comprehensive analysis of the Bencao (herbal) small RNA Atlas reveals novel RNA therapeutics for treating human diseases.Science China. Life sciences · 2023Article
67 more citing papers are in PubMed but not listed here.
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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.
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