The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Abstract

Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A 1 Tcontent equals two at their immediate adjacent sites; and (3) C 4 Tand A 4 G transitions have reverse complementary neighborhood patterns and so do A 4 C and G 4 T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C 4 T/ A 4 G and A 4 C/G 4 T, the true neighborhood patterns for A 4 T and C 4 G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A 1 T and G 1 C was quite different. The ratio was lowest for C 4 G, but increased for C 4 T/A 4 G, further for A 4 C/G 4 T, and the most for A 4 T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A 4 G and C 4 T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for $20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

Comparative Analysis of Kabuli Chickpea Transcriptome with Desi and Wild Chickpea Provides a Rich Resource for Development of Functional Markers

“…The greater number of transitions as compared to transversions is consistent with previous reports [6], [42], [43]. Hyper-mutability of CpG islands and more synonymous mutations resulting due to transitions are the primary reasons attributed to higher proportion of transitions than transversions [44]–[46]. A significant number of these SNPs were detected in tissue-specific and transcription factor encoding transcripts.…”

A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)

“…Most SNPs were bi‐allelic but a small number were tri‐allelic (0.6%). There were 63.3% transitions and 36.6% transversions, giving a ratio of 1.73 transitions to transversions, which is similar to that found in cattle (1.81; Jiang et al. 2008), but lower than the ratio in chicken (2.3; Vignal et al.…”

High‐throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform

“…, 2003). The hyper‐mutability of CpG islands is considered as a primary reason for higher proportion of transitions than transversions in exons present in plant as well as animal genomes (Duncan and Miller, 1980; Jiang et al. , 2008).…”