Mitochondrial genome dataset of Drosophila melanogaster Meigen, 1830 (fruit fly) from Pakistan

<i>Drosophila melanogaster</i> is one of the most employed animal models and was amongst the first organisms selected for genome sequencing. Geographically isolated populations of <i>D. melanogaster</i> have shown to harbour distinct allelic makeup. In this data article, we present the whole mitochondrial draft genome sequence of a white eye mutant of <i>D. melanogaster</i>, dubbed as ANU-1. The strain was isolated from wildtype population. This is the first report of the mitochondrial genome of <i>D. melanogaster</i> from Pakistan. The complete mitochondrial genome of <i>D. melanogaster</i> ANU-1 is 19,116 bp in length containing 13 protein coding genes, 22 tRNA genes, 2 rRNA genes and an AT-rich region of 4208 bp in length. Phylogenetic analysis based on mitochondrial DNA sequences clustered <i>D. melanogaster</i> ANU-1 with other species of melanogaster subgroup. Genome sequence comparison identified novel alleles in <i>COX1, ND5</i> and <i>CYTB</i> genes in <i>D. melanogaster</i> ANU-1 with subtle structural variations in the encoded proteins. The present mitochondrial genome provides the first glimpse of allelic variations in <i>D. melanogaster</i> from Pakistan and was deposited in GenBank under the accession number OR555819.1.