Bioinformatic study of the Phylogeny of house mouse complex (Mus musculus) using mitochondrial genome of D-loop region (mtDNA) and Cytochrome b & c

Mus musculus is a valuable laboratory model more than a century and in the worldwide studies have been done about it. There are three main subspecies Mus musculus with the scientific name (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus) with worldwide distribution. There are several theories about the origin of subspecies Mus musculus one of which Iran is referred to as the origin. To study Bioinformatics and phylogenetic species Phylogeography complex Mus musculus mtDNA sequence was 1730, including 1330 D-loop sequences and 400 sequences of cytochrome b, and c (310 cytochrome b sequences and 90 sequences of cytochrome c), Using the mitochondrial sequences, performed phylogenetic analyzes and draw trees and were examined the subspecies Mus musculus. The amino acid sequences of cytochrome b and c three-dimensional shapes were analyzed by using phylogenetic and Bioinformatics software. Population genetic analyzes showed that Iran is an origin of complex Mus musculus, and haplotypes were identified by evolutionary paths and ancestral haplotype was examined in Iran. Bioinformatics amino acid analysis results showed that cytochrome b is cytochrome variable and subunits of cytochrome c have the fewest changes. As part of the cytochrome b, which is located in the cytoplasm of the cell is significantly more amino acid changes. The results showed that the protected areas are not exclusive to D-loop and different cytochrome regions have protected areas. Using cytochrome b and c amino acids changes in each subspecies and it can be used as reliable indicators for detection and a stable model to identifying the subspecies Mus musculus.