Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.

ABSTRACT: Patterns of non-uniform usage of synonymous codons vary across genes in an organism and between species across all domains of life. This codon usage bias (CUB) is due to a combination of non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most models quantify the effects of mutation bias and selection on CUB assuming uniform mutational and other non-adaptive forces across the genome. However, non-adaptive nucleotide biases can vary within a genome due to processes such as biased gene conversion (BGC), potentially obfuscating signals of selection on codon usage. Moreover, genome-wide estimates of non-adaptive nucleotide biases are lacking for non-model organisms. We combine an unsupervised learning method with a

SUBMITTER: Cope AL 

PROVIDER: S-EPMC9246145 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature