Title:SNP-based Computational Analysis Reveals Recombination-associated
Genome Evolution in Humans
Volume: 18
Issue: 2
Author(s): Qiguo Zhang and Guoqing Liu*
Affiliation:
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
- Inner Mongolia Key Laboratory of Functional Genomics and Bioinformatics, Inner Mongolia University of Science and Technology,
Baotou, China
Keywords:
Meiotic recombination, gene conversion, genetic diversity, DSB, neighbor-dependent mutational bias, recombination rate.
Abstract:
Background: Meiotic recombination is an important source of genetic variation, but how recombination
shapes the genome is not clearly understood yet.
Objective: Here, we investigate the roles of recombination on human genome evolution from two aspects:
How does recombination shape single nucleotide polymorphism (SNP)-related genomic variation
features? Whether recombination drives genome evolution through a neighbor-dependent mutational bias?
Methods: We analyzed the relationship of recombination rate with mutational bias and selection effect
at SNP sites derived from the 1000 Genomes Project.
Results: Our results show that SNP density, Ts/Tv, nucleotide diversity, and Tajima's D were positively
correlated with the recombination rate, while Ka/Ks were negatively correlated with the recombination
rate. Moreover, compared with non-coding regions, gene exonic regions have lower nucleotide diversity
but higher Tajima's D, suggesting that coding regions are subject to stronger negative selection but have
fewer rare alleles. Gene set enrichment analysis of the protein-coding genes with extreme Ka/Ks ratio
implies that under the effect of high recombination rates, the genes involved in the cell cycle, RNA processing,
and oocyte meiosis are subject to strong negative selection. Our data also support S (G or C) >
W (A or T) mutational bias and W>S fixation bias in high recombination regions. In addition, the
neighbor-dependent mutational bias was found to be stronger at high recombination regions.
Conclusion: Our data suggest that genetic variation patterns, particularly the neighbor-dependent mutational
bias at SNP sites in the human genome, are mediated by recombination.
