A cross-talk on compositional dynamics and codon usage patterns of mitochondrial CYB gene in Echinodermata

Codon usage bias (CUB) refers to a phenomenon in which some synonymous codons are used in mature mRNA at a higher frequency than other members codifying the same amino acid. CUB is mainly determined by mutation pressure and natural selection. We used bioinformatic tools to analyze the protein coding sequences of mitochondrial CYB gene in different classes of Echinodermata to understand the patterns of codon usage. The ENC values of CYB gene in five different classes of Echinodermata were 41.64, 30.33, 43.63, 41.11, and 41.33, which suggested that the CUB of this gene was low. The relative synonymous codon usage (RSCU) values showed that the patterns of over-represented and under-represented codons were different among different classes. Correspondence analysis indicated that the plots of CYB gene were different across classes, suggesting that the pattern of codon usage was also different among five classes under study. Highly significant correlation (p < .01) between overall nucleotide composition and its 3rd codon position indicated that both mutational pressure and natural selection had an influence on the codon usage bias of CYB gene. Furthermore, PR-2 bias plot analysis showed that both mutation pressure and natural selection might have affected the pattern of codon usage in CYB gene of Echinodermata.