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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.

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