Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 ( is one essential gene for autophagy initiation, yet the evolutionary trends of the gene at the usages of nucleotide and synonymous codon remains unexplored. According to phyloge...

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Bibliographic Details
Published in:Frontiers in cellular and infection microbiology 2021-11, Vol.11, p.771010-771010
Main Authors: Li, Yicong, Wang, Rui, Wang, Huihui, Pu, Feiyang, Feng, Xili, Jin, Li, Ma, Zhongren, Ma, Xiao-Xia
Format: Article
Language:English
Subjects:
Animals
autophagy-related gene 13
Autophagy-Related Proteins - genetics
Cellular and Infection Microbiology
Codon Usage
Eukaryota - genetics
Evolution, Molecular
nucleotide composition distribution
nucleotide usage
Nucleotides - genetics
phylogenetic analyses
Phylogeny
synonymous codon usage
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Summary:Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 ( is one essential gene for autophagy initiation, yet the evolutionary trends of the gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the genes. Furthermore, the bias level of nucleotide 'G' usage is highest, while that of nucleotide 'C' usage is lowest in the genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals ( , ) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the gene display that natural selection still dominates codon usages during organisms' evolution.
ISSN:2235-2988
2235-2988
DOI:10.3389/fcimb.2021.771010