Analysis of the Genetic and Phylogenetic Structure of the Mitochondrial Genome of Wild and Domestic Goat Species

DNA Mitochondria is one of the most commonly molecular markers for phylogenetic studies in animals due to its simple genome structure, which presents an ideal model to study evolution and genetic similarity. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the eight species of wild and domestic goat based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.

In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes per each genome from seven wild species of goat including Markhor (C. falcoeri), Capra ibex, Capra nubiana, Capra pyrenaica, Capra sibirica, Capra caucasica, Capra aegagrus, and domesticated species of goat (Capra hircus) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software.

Based on the analysis, it was found that the highest similarity between the nucleotide sequences of the complete genome (99.50) of domestic goat (Capra hircus) and wild Capra aegagrus goat and the lowest percentage of similarity (93.79) between the nucleotide sequences of the complete genome of the breed Capra nubiana) with wild goat Capra sibirica goat. Also, based on the results of the phylogenetic tree, it was found that domestic goat breeds (Capra hircus) and wild Capra aegagrus goat are divided into one group and wild Capra ibex and Capra pyrenaica breeds are divided into another distinct cluster.

In this study, all the results obtained from complete sequences of the mitochondrial genome analysis are consistent with the results obtained from the sequence of 13 protein coding genes per each genome, which indicates the correct clustering of wild and domestic goat breeds. Therefore, mitochondrial genome sequences could be used as a suitable genetic marker for accurate phylogenetic analysis and clustering of different species of sheep.