ArticleNature communications2017
Sequencing and de novo assembly of a near complete indica rice genome.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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Who cites it
151 citing papers in PubMed.
- Genome-wide prediction of cloned disease resistance homologues across the Oryza genus.The plant genome · 2026Article
- Whole Genome Sequencing of the Moruga Hill Rice (Biotech (Basel (Switzerland)) · 2026Article
- A portable recalibration workflow for reference-based variant calling in non-human genomes.PLoS computational biology · 2026Article
- The Genome of the Rice Variety Mowanggu Provides Insight Into Resistance to Magnaporthe oryzae.Molecular plant pathology · 2026Article
- Structural Variations Contribute to Subspeciation and Yield Heterosis in Rice.Plant biotechnology journal · 2025Article
- Genomic and translational insights into eIF2B-mediated salt tolerance in sea rice HD961.BMC biology · 2025Article
- Evolutionary histories of functional mutations during the domestication and spread ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Allele Mining of Seed-Related Genes Reveals Early movement, Selection and Adaptation of Asian Rice Landraces.Rice (New York, N.Y.) · 2025Article
- Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents.Rice (New York, N.Y.) · 2025Article
- The origin and evolution of cultivated rice and genomic signatures of heterosis for yield traits in super-hybrid rice.BMC biology · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- Maladaptation in cereal crop landraces following a soot-producing climate catastrophe.Nature communications · 2025Article
- Chromosomal structural variation loci HSS1 and HSS6 lead to hybrid sterility in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis.Rice (New York, N.Y.) · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- A full genome assembly reveals drought stress effects on gene expression and metabolite profiles in blackcurrant (Horticulture research · 2025Article
- Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).G3 (Bethesda, Md.) · 2025Article
- A gapless genome assembly of aFrontiers in plant science · 2025Article
- Genome evolution and diversity of wild and cultivated rice species.Nature communications · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
91 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.
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