Codon bias in the mitochondrial genomes of two invasive Gambusia species

【Objective】The mitochondrial genome composition and codon usage bias of Gambusia affinis and G. holbrooki were studied in order to provide theoretical basis for early warning，prevention and control of invasive Gambusia species.【Method】Based on the mitochondrial genome sequence data，the mitochondrial genome composition characteristics and codon usage patterns of G. affinis and G. holbrooki were analyzed by bioinformatics methods.【Result】The mitochondrial genome sizes of G. affinis and G. holbrooki were 16614 and 16610 bp with obvious AT bias in their base composition. The codon adaptation index（CAI）ranged for protein-coding genes were 0.14 to 0.20 for G. affinis and 0.13 to 0.20 for G. holbrooki. The values of codon bias index（CBI）ranged from -0.09 to 0.09 and -0.09 to 0.07，respectively. The effective number of codon（ENC）ranged from 35.19 to 50.5 and 39.03 to 50.06，respectively. There was no obvious correlation between GC contents of the 1^st，2^nd，and 3^rd bases of mitochondrial coding genes in both species based on neutrality plot analysis. ENC-plot revealed that ENC values of mitochondrial genes in two species were both located below the standard curve. PR2-plot analysis found that the usage frequency of the four bases at the 3^rd codon position in mitochondrial genes was not equal，the usage frequency of A and C was higher than T and G. Sixteen and eighteen optimal codons in the mitochondrial genome of G. affinis and G. holbrooki were identified，respectively.【Conclusion】The mitochondrial genomes of the two Gambusia species prefer to use codons ending with C or A，and without G endings. Sixteen and eighteen optimal codons in the mitochondrial genome of G. affinis and G. holbrooki are identified，mainly ending with C or A. The results suggest that codons in the mitochondrial genome of G. affinis and G. holbrooki show weak bias. Natural selection and mutation pressure play an important role in the forming codon bias in the mitochondrial genome for the two Gambusia species，with natural selection being the more influencing factor