Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species

Codon basis is a common and complex natural phenomenon observed in many kinds of organisms. In the present study, we analyzed the base bias of 12 mitochondrial core protein-coding genes (PCGs) shared by nine species. The results showed that the codons of all species tended to end in A/T, demonstrating the preference of mitochondrial codons of species for a preference for this codon. In addition, we detected the correlation between codon base composition and the codon adaptation index (CAI), codon bias index (CBI), and frequency of optimal codons (FOP) indices, indicating the influence of base composition on codon bias. The average effective number of codons (ENC) of mitochondrial core PCGs of is 30.81, which is 0.08 and RSCU > 1) in nine species, and GCA and AUU were the most widely used optimal codons. Based on the combined mitochondrial sequence and RSCU value, we deduced the genetic relationship between different species and found large variations between them. This study promoted the understanding of synonymous codon usage characteristics and evolution of this important fungal group.