Mitochondrial genome diversity among jungle fowl and domestic chicken

Nucleotide sequence variability was studied in complete mitochondrial DNA sequences from different red jungle fowl subspecies i.e. Gallus gallus gallus, Gallus gallus bankiva, Gallus gallus spadiceus and domestic fowl i.e. Gallus gallus domesticus. The total mitochondrial genome ranged from 16784 bp to 16788 bp. Very low polymorphism (0.47%) was observed between the different G. g. subspecies including G. g. domesticus. The tRNA genes showed high degree of conservation. All other mitochondrial genes, except ATPase8, showed sequence variability, however it was very low in magnitude (0.220 to 1.347%). In control region (D loop), the percent polymorphism was 1.35%. Majority of the nucleotide substitutions (~94%) were transitions. Out of the 67 nucleotide substitutions, 19 were specific to G. g. domesticus and may be used as population specific markers. Phylogenetic tree based on whole mitochondrial DNA nucleotide sequence variability showed the clustering of all the G. g. domesticus sequences in one cluster, while other G. g. subspecies in another, revealing the almost equal distances between G. g. domesticus and other G. g. subspecies. The results revealed that though there is low amount of genetic variability between red jungle fowl and domestic fowl, but, some SNPs specific to G. g. domesticus might be used as population specific markers.