Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

Abstract

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

“…GC heterogeneity and gBGC can lead to codon usage bias, which is a consequence of local recombination rate-based codon usage ( Palidwor et al, 2010 ; Oldfield et al, 2020 ). Mutations, natural selection, and genetic drift are all factors that contribute to the development of synonymous codons and thus have a considerable effect on genome evolution ( Li et al, 2018 ; Li B. et al, 2022 ). It has been proposed that interspecific differences in codon usage can be explained by a mutation mechanism in which codon bias is caused by the rate of repair of nucleotide bias or point mutations ( LaBella et al, 2019 ; Lamolle et al, 2022 ; Li et al, 2022c , 2023b ).…”

The nucleotide usages significantly impact synonymous codon usage inMycoplasma hyorhinis

“…However, the analyses of codon usage show that codon usage preference is not random and the genetic characteristic represented by codon usage bias (CUB) can be primarily and plausibly explained by two dominant evolutionary dynamics: directional mutation pressure on nucleotide sequences (either toward AT or GC) and natural selection affecting mRNA stability and gene expression [6][7][8]. The analysis of codon usage patterns has previously been employed to reveal a specific genetic background, which can reflect the role of nucleotide usage in the organism of interest [9][10][11][12][13][14].…”