Figure 6. Neutrality plot for Hsp60 genes of Chordata
As can be seen, the Hsp60 genes can be divided into two groups. The AT-biased group includes the Hsp60 genes from Mammalia, Aves, Reptilia, and Amphibia. In turn, the second group with GC-bias includes all Hsp60 genes from Fish and five Hsp60 genes belonging to Hyperoartia (Petromyzon marinus , GC3 0.92), Mammalia (Ornithorhynchus anatinus , GC3 0.88;Lipotes vexillifer , GC3 0.76), and Leptocardii (Branchiostoma floridae , GC3 0.62; Gekko japonicus , GC3 0.52). Interestingly, four of these organisms, with the exception of Gekko japonicus , are aquatic. On the other hand, there is the Hsp60 gene from Boleophthalmus pectinirostris , belonging to Fish, with GC3 of 0.496, which is closest to the equilibrium GC3 of Chordata. This mudskipper is an amphibious fish capable of feeding on land. It has been suggested that codon usage bias due to substitutions of synonymous codons may be associated with the lifestyle of organisms54–56. Based on this, we can assume that the habitat or specific diet can influence the synonymous codon substitution in the Hsp60 genes of the mentioned organisms.
Neutrality of codon usage for all phyla, with the exception of Euryarchaeota, was less than 20%, indicating that natural selection dominates mutational pressure at the third position of codons in these Hsp60 genes (Table 2). At the same time, the neutrality of 32.4% for the Hsp60 genes from Euryarchaeota is the highest among all 17 phyla and indicates a rather high degree of mutational pressure. The high correlation coefficient R of 0.865 reflects the important role of mutational pressure as a factor affecting codon usage57.
Thus, the high resistance to spontaneous mutations provided by DNA repair systems, low mutational pressure, and constant amino acid composition (see Amino acid composition of Hsp60) suggest that the Hsp60 gene is a trait inherent in all organisms58.