Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs

Publication date: Available online 23 December 2019Source: Journal of Genetics and GenomicsAuthor(s): Wen-Hong Zu, Hang Zhang, Xun Lan, Xu TanAbstractNoncoding RNAs play important roles in many biological processes and provide material for evolutionary adaptations beyond protein-coding genes, such as in the arms race between host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated noncoding RNAs is not available. Here we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable to those of the established codon-based method and phyloP method for coding genes; thus, it provides a holistic framework for estimating the selection on the entire genome. We further show that fast-evolving protein-coding genes and their corresponding 5′ untranslated regions have a significantly lower frequency of the CpG dinucleotide than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.

Source: Journal of Genetics and Genomics - December 24, 2019 Category: Genetics & Stem Cells Source Type: research