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

Frontiers in Cellular and Infection Microbiology

Yicong Li¹  Xili Feng¹  Li Jin¹  Huihui Wang¹  Zhongren Ma¹  Xiao-xia Ma¹  Feiyang Pu¹  Rui Wang² 

[1] Biomedical Research Center, Northwest Minzu University, Lanzhou, China;Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States;

关键词: autophagy-related gene 13;    phylogenetic analyses;    nucleotide usage;    synonymous codon usage;    nucleotide composition distribution;   

DOI  :  10.3389/fcimb.2021.771010

来源: Frontiers

【 摘 要 】

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 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 atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

【 授权许可】

CC BY