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https://doi.org/10.1038/srep27272
Title: | Purifying selection shapes the coincident SNP distribution of primate coding sequences | Authors: | Chen, C.-Y Hung, L.-Y Wu, C.-S Chuang, T.-J |
Keywords: | animal DNA sequence genetic database genetic selection genetics human molecular evolution mutation rate Pan troglodytes procedures single nucleotide polymorphism Animals Databases, Genetic Evolution, Molecular Humans Mutation Rate Pan troglodytes Polymorphism, Single Nucleotide Selection, Genetic Sequence Analysis, DNA |
Issue Date: | 2016 | Publisher: | Nature Publishing Group | Citation: | Chen, C.-Y, Hung, L.-Y, Wu, C.-S, Chuang, T.-J (2016). Purifying selection shapes the coincident SNP distribution of primate coding sequences. Scientific Reports 6 : 27272. ScholarBank@NUS Repository. https://doi.org/10.1038/srep27272 | Rights: | Attribution 4.0 International | Abstract: | Genome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (coSNPs) at human-chimpanzee orthologous positions, and suggested that this is due to cryptic variation in the mutation rate. While this phenomenon primarily corresponds with non-coding coSNPs, the situation in coding sequences remains unclear. Here we calculate the observed-to-expected ratio of coSNPs (coSNPO/E) to estimate the prevalence of human-chimpanzee coSNPs, and show that the excess of coSNPs is also present in coding regions. Intriguingly, coSNPO/E is much higher at zero-fold than at nonzero-fold degenerate sites; such a difference is due to an elevation of coSNPO/E at zero-fold degenerate sites, rather than a reduction at nonzero-fold degenerate ones. These trends are independent of chimpanzee subpopulation, population size, or sequencing techniques; and hold in broad generality across primates. We find that this discrepancy cannot fully explained by sequence contexts, shared ancestral polymorphisms, SNP density, and recombination rate, and that coSNPO/E in coding sequences is significantly influenced by purifying selection. We also show that selection and mutation rate affect coSNPO/E independently, and coSNPs tend to be less damaging and more correlated with human diseases than non-coSNPs. These suggest that coSNPs may represent a "signature" during primate protein evolution. | Source Title: | Scientific Reports | URI: | https://scholarbank.nus.edu.sg/handle/10635/182464 | ISSN: | 2045-2322 | DOI: | 10.1038/srep27272 | Rights: | Attribution 4.0 International |
Appears in Collections: | Elements Staff Publications |
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