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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
molecular evolution
mutation rate
Pan troglodytes
single nucleotide polymorphism
Databases, Genetic
Evolution, Molecular
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.
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
ISSN: 2045-2322
DOI: 10.1038/srep27272
Rights: Attribution 4.0 International
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