Genetic Diversity of atp6 and cox3 Gene in Wild Drosophila melanogaster

Mitochondria are the energy factory in cells, and more than 95% of the energy in cells is produced by the mitochondrial oxidative phosphorylation (OXPHOS). Therefore, mitochondria likely plays an important role in the process of high-altitude adaptation. Wild Drosophila melanogaster population structure provides a good precondition to detect positive selection on mitochondrial genes related to environmental or climatic variation, specifically hypoxia and high altitudes. In this paper, we sequenced atp6 (ATPase synthase 6) from 27 individuals and cox3 (cytochrome c oxidase III) from 26 individuals of wild Drosophila melanogaster. The percent G+C content of atp6 and cox3 genes has a value of 24 and 29.3%, respectively, exhibiting an extreme bias in base composition. 5 single nucleotide polymorphisms (SNPs) were detected and 2 nonsynonymous substitutions (m.555T > A and m.577A > G) were detected in atp6, only one SNP (m.126C > T) was found from highland Drosophila melanogaster. 6 SNPs were detected in cox3, we found 2 nonsynonymous substitutions (m.745G > A and m.427G > A) of only one highland strain from Yun Nan province. Substitution rates and dN/dS ratios were relatively high for cox3 ( = 0.34851) compared to atp6 ( = 0.07329), both of them inferring is purifying selection by using PAML. Only one amino acid site 255I (p < 0.01) of the cox3 gene was found in one fly from low altitude Drosophila sample, which was generated by SNPs (m.763A > G and m.764T > C). From these analyses we conclude that selection may not have played a role in shaping Drosophila melanogaster regional mtDNA variation, the changes in selection is very likely due to some environmental stressors other than hypoxia and high altitudes, and more broadly, our results add to an emerging body of research in Drosophila.