ArticleMolecular genetics and genomics : MGG2008
The pattern of insertion/deletion polymorphism in Arabidopsis thaliana.
Article in Molecular genetics and genomics : MGG, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Different genomic footprint of small insertion-deletion and structural variants determines the genetic divergence of indica and japonica rice.BMC genomics · 2026Article
- Article
- The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice.International journal of molecular sciences · 2022Article
- Alteration of synonymous codon usage bias accompanies polyploidization in wheat.Frontiers in genetics · 2022Article
- Field Screen and Genotyping ofInsects · 2021Article
- Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat.Frontiers in genetics · 2021Article
- Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome.Frontiers in genetics · 2021Article
- Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat.PloS one · 2020Article
- Mutational Dynamics of Aroid Chloroplast Genomes II.Frontiers in genetics · 2020Article
- The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat.BMC plant biology · 2018Article
- Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice.Scientific reports · 2018Article
- Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution.PloS one · 2015Article
- Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.Evolutionary bioinformatics online · 2015Article
- Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants.BMC genomics · 2013Article
- Evolutionary genomics of Colias Phosphoglucose Isomerase (PGI) introns.Journal of molecular evolution · 2012Article
- Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.PLoS biology · 2011Article
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Authors and funding
6 authors.
Funding
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Abstract
Little is known about variation of nucleotide insertion/deletions (indels) within species. In Arabidopsis thaliana, we investigated indel polymorphism patterns between two genome sequences and among 96 accessions at 1215 loci. Our study identified patterns in the variation of indel density, size, GC content and distribution, and a correlation between indels and substitutions. We found that the GC content in indel sequences was lower than that in non-indel sequences and that indels typically occur in regions with lower GC content. Patterns of indel frequency distribution among populations were more consistent with neutral expectation than substitution patterns. We also found that the local level of substitutions is positively correlated with indel density and negatively correlated with their distance to the closed indel, suggesting that indels play an important role in nucleotide variation.
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