Exploring mitochondrial genome sequence of swamp deer subspecies ( Rucervus Duvaucelii ): comparative and phylogenetic insights

The comparative characterization of the complete mitogenome of three subspecies of the genus Rucervus duvaucelii revealed close genetic relationship among Rucervus duvaucelii duvaucelii, Rucervus duvaucelii branderi and Rucervus duvaucelii ranjitsinhii. Three mitogenome of Rucervus duvaucelii branderi were sequenced by next generation sequencing without the use of mitogenome-specific primers and measured 16407 bp, 16412 bp and 16361 bp. These three sequences of Rucervus duvaucelii duvaucelii (n = 3) were compared with seven previously reported Rucervus mitogenomes derived by Sanger sequencing using specific primers. The length of coding genes (CGs) in all the three subspecies ranged from 11461 bp to 11403 bp accounting for 69.77-69.85% of the mitogenome. The A + T content of the 13 CGs in the mitogenome were comparable among the three subspecies. All transfer RNA gene sequences formed secondary cloverleaf structures except trnSer2 and G + C content of the tRNA genes varied from 20.3% (trnArg) to 45.2% (trnAsn). Two hepta nucleotide motifs (‘ttttccc’ and ‘gtacata’) were observed in the control region. The atp8 gene presented the highest evolutionary rate, with a dN/dS ratio of (0.348) whereas cox1 exhibited the lowest (0.0106). The phylogenetic tree highlighted the evolutionary significance of the genus Rucervus and all the ten whole mitochondrial genome sequences were clustered together.