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.hol-brooki 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 characteris-tics and codon usage patterns of G.affinis and G.holbrooki were analyzed by bioinformatics methods.[Result]The mito-chondrial genome sizes of G.affinis and G.holbrooki were 16614 and 16610 bp with obvious AT bias in their base compo-sition.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 ef-fective number of codon(ENC)ranged from 35.19 to 50.5 and 39.03 to 50.06,respectively.There was no obvious correla-tion between GC contents of the 1st,2nd,and 3rd 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 stan-dard curve.PR2-plot analysis found that the usage frequency of the four bases at the 3rd 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 ge-nomes of the two Gambusia species prefer to use codons ending with C or A,and without G endings.Sixteen and eigh-teen 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 selec-tion and mutation pressure play an important role in the forming codon bias in the mitochondrial genome for the two Gam-busia species,with natural selection being the more influencing factor.
万方数据
维普
