ArticleProceedings of the National Academy of Sciences of the United States of America2014
Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon.Nature communications · 2022Article
- Nonhomologous end joining as key to CRISPR/Cas-mediated plant chromosome engineering.Plant physiology · 2022Article
- Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants.The Plant cell · 2021Article
- A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini.Nature communications · 2021Article
- Gene disruption by structural mutations drives selection in US rice breeding over the last century.PLoS genetics · 2021Article
- Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.Genome biology and evolution · 2020Article
- Article
- BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining.Nature communications · 2020Article
- Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution.Cells · 2020Review
- Mutagenesis in Rice: The Basis for Breeding a New Super Plant.Frontiers in plant science · 2019Review
- Birth and Death of LTR-Retrotransposons inGenetics · 2018Article
- Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars.Genome biology · 2018Article
- Mutational signatures of non-homologous and polymerase theta-mediated end-joining in embryonic stem cells.The EMBO journal · 2017Article
- Genetic Analysis of Natural Variation inFrontiers in plant science · 2017Article
- Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- The impact and origin of copy number variations in the Oryza species.BMC genomics · 2016Article
- Acquired Flucytosine Resistance during Combination Therapy with Caspofungin and Flucytosine for Candida glabrata Cystitis.Antimicrobial agents and chemotherapy · 2016Article
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2 authors.
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Abstract
The insertion of DNA into a genome can result in the duplication and dispersal of functional sequences through the genome. In addition, a deeper understanding of insertion mechanisms will inform methods of genetic engineering and plant transformation. Exploiting structural variations in numerous rice accessions, we have inferred and analyzed intermediate length (10-1,000 bp) insertions in plants. Insertions in this size class were found to be approximately equal in frequency to deletions, and compound insertion-deletions comprised only 0.1% of all events. Our findings indicate that, as observed in humans, tandem or partially tandem duplications are the dominant form of insertion (48%), although short duplications from ectopic donors account for a sizable fraction of insertions in rice (38%). Many nontandem duplications contain insertions from nearby DNA (within 200 bp) and can contain multiple donor sources--some distant--in single events. Although replication slippage is a plausible explanation for tandem duplications, the end homology required in such a model is most often absent and rarely is >5 bp. However, end homology is commonly longer than expected by chance. Such findings lead us to favor a model of patch-mediated double-strand-break creation followed by nonhomologous end-joining. Additionally, a striking bias toward 31-bp partially tandem duplications suggests that errors in nucleotide excision repair may be resolved via a similar, but distinct, pathway. In summary, the analysis of recent insertions in rice suggests multiple underappreciated causes of structural variation in eukaryotes.
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