ArticleBMC genomics2016
The impact and origin of copy number variations in the Oryza species.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Comprehensive characterization and diversity analysis of the HIS1 gene family in rice subpopulations for herbicide resistance.BMC plant biology · 2025Article
- Plant Kinesin Repertoires Expand with New Domain Architecture and Contract with the Loss of Flagella.Journal of molecular evolution · 2024Article
- Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing.Genome biology · 2024Article
- Article
- An evolutionary look into the history of lentil reveals unexpected diversity.Evolutionary applications · 2022Article
- In-Depth Sequence Analysis of Bread WheatInternational journal of molecular sciences · 2021Article
- Calling large indels in 1047 Arabidopsis with IndelEnsembler.Nucleic acids research · 2021Article
- Article
- Structural variations in papaya genomes.BMC genomics · 2021Article
- How the pan-genome is changing crop genomics and improvement.Genome biology · 2021Review
- Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species.Frontiers in plant science · 2021Article
- Segmental duplications are hot spots of copy number variants affecting barley gene content.The Plant journal : for cell and molecular biology · 2020Article
- Structural genome analysis in cultivated potato taxa.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- The Copy Number Variation ofFrontiers in plant science · 2020Article
- Structural variants in 3000 rice genomes.Genome research · 2019Article
- Simultaneous regulation of F5H in COMT-RNAi transgenic switchgrass alters effects of COMT suppression on syringyl lignin biosynthesis.Plant biotechnology journal · 2019Article
- Connecting genome structural variation with complex traits in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Copy number variation and disease resistance in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
- Dosage sensitivity is a major determinant of human copy number variant pathogenicity.Nature communications · 2017Article
- CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation.BMC genomics · 2017Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice.
resultsHere, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome 'Nipponbare'. Using Oryza glaberrima as the outgroup, 80% of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion.
conclusionsThis study showed the impact and origin of copy number variations in rice on a genomic scale.
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