Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

McDonald, Michael J.; Wang, Wei-Chi; Huang, Hsien-Da; Leu, Jun‐Yi

doi:10.1371/journal.pbio.1000622

Cited by 115 publications

(127 citation statements)

References 39 publications

(58 reference statements)

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“…As observed previously (Tian et al 2008;McDonald et al 2011;Massouras et al 2012;Jovelin and Cutter 2013), we found a strong positive correlation between the genomic distribution of indels and SNPs. These correlated patterns of polymorphism are, in turn, correlated with local recombination, suggesting that the nonrandom distributions are due to hitchhiking and background selection (Begun and Aquadro 1992;Charlesworth et al 1993).…”

Section: Discussionsupporting

confidence: 90%

“…Several biological mechanisms have been proposed for the clustering of SNPs and indels, which appears to be ubiquitous in prokaryotes and eukaryotes (Tian et al 2008;Hodgkinson and Eyre-Walker 2011;McDonald et al 2011;Jovelin and Cutter 2013). Possibly indels (Tian et al 2008;Jovelin and Cutter 2013) and repeats (McDonald et al 2011) are mutagenic because they induce error-prone DNA polymerase replication near the indel or repeat (Yang and Woodgate 2007); the regions in which SNPs and indels occur are inherently mutagenic; or SNPs and indels are subject to the same population genomic processes.…”

Section: Nonrandom Distribution Of Snps and Indelsmentioning

confidence: 99%

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Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

et al. 2014

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The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/ deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.[Supplemental material is available for this article.]Studies in Drosophila melanogaster have revealed basic principles and mechanisms underlying fundamental genetic concepts of linkage and recombination and were instrumental in identifying canonical and evolutionarily conserved cell signaling pathways.Most D. melanogaster genes are evolutionarily conserved, leading to fly models for understanding common human diseases and behavioral disorders, dipteran disease vectors, and insects impacting agriculture, medicine, and forensics. Despite nearly a century of research on D. melanogaster, however, a large fraction of its coding and noncoding sequence has no known function (McQuilton et al. 2012). Recent efforts to induce mutations in every protein coding gene utilize transposable elements (Bellen et al. 2004(Bellen et al. , 2011, which have a different spectrum of allelic effects than SNPs and small insertions and deletions (indels). Comprehensive efforts to identify regulatory DNA elements in Drosophila (The Ó 2014 Huang et al.

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Section: Discussionsupporting

confidence: 90%

Section: Nonrandom Distribution Of Snps and Indelsmentioning

confidence: 99%

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

et al. 2014

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“…Were this to be the case, we would expect that SVs with higher minor allele frequency (MAF) in the population would result in higher nucleotide diversity in their vicinity. However, in this study, we found that the nucleotide diversity was similar in the flanking regions of SVs with different MAFs ( Figure 2C), implying that SVs in cucumber might not be mutagenic agents, which is similar to a previous report (McDonald et al, 2011). It is worth noting that the higher nucleotide diversity in the vicinity of SVs might be caused to some extent by the potentially high rate of false SNP calls due to inaccurate read mapping near SVs.…”

Section: Mechanisms Of Sv Formationsupporting

confidence: 86%

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

et al. 2015

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Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated breakinduced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.

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“…Although the regional effect is also of great impor tance; that is, indels occur more frequently in the sites that are more susceptible to nucleotide substitutions (McDonald, 2011). Despite the prevalence of trans versions among the nucleotide substitutions, it should be noted that their distribution is almost unrelated to the presence of indels, and transversions accumulate primarily in the species that are morphologically more distant.…”

Section: Discussionmentioning

confidence: 99%

Genetic and morphological diversification in gastropods of the Baicaliidae family

Kovalenkova

Sitnikova

Sherbakov

2015

Russ J Genet Appl Res

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The combined ("total evidence") phylogenetic inference was based on the comparison of the intronic nucleotide sequences of the ATP synthase α subunit gene of 11 gastropod species belonging to the rapidly evolving Baikalian endemic family Baicaliidae, the morphological description of these species, and the previously published sequences of the mitochondrial gene coding the first subunit of cytochrome c oxi dase. The phylogeny based on the intron sequences agrees well with the morphology. It is shown that sister species usually have similar substrate preferences. Certain discrepancy in the phylogenetic tree topology and the taxonomy based on morphological traits is probably due to the rapid morphological evolution of mollusks of the family Baicaliidae.

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Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

Abstract: The authors propose that short repeat sequences may play an important role in causing the pervasive clustering of mutations across diverse genomes from prokaryotes to humans.

Cited by 115 publications

References 39 publications

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

Genetic and morphological diversification in gastropods of the Baicaliidae family

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