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<p>In India, the sambardeer&#xa0;(<i>Rusa unicolor</i>), barking deer (<i>&#xa0;Muntiacus muntjak</i>), spotted deer (<i>Axis axis</i>), and Indian mouse deer (<i>Moschiola indica,&#xa0;Artiodactyla: Tragulidae</i>) are widely distributed. Deer are often poached for bush meat, skin, antlers and other purposes. The mitochondrial genome is essential for species identification and understanding evolutionary relationships. Therefore, sequencing the complete mitochondrial genome of deer species is vital for rapid species identification and conservation efforts. This study aimed to sequence the complete mitochondrial genomes of spotted and sambar deer using Next-Generation Sequencing technology. The results revealed the size of the complete mitochondrial genome (mt-DNA) of spotted deer (16,351&#xa0;bp) and sambar deer (16,476&#xa0;bp), respectively. Each mt-DNA encompassed 37 genes <i>viz</i> 13 Protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. The comparative analysis of mitochondrial nucleotide composition between <i>Axis</i> and <i>Rusa</i> species revealed closely similar ratios of A + T and G + C. Two complementary approaches (Maximum Likelihood and Bayesian Inference) were used to understand the phylogenetic relationship among Cervidae. The results indicated that the <i>A. axis</i> consistently formed a well-supported clade with bootstrap values of 100 and posterior probabilities of 1.000, which were closely related to <i>A. porcinus</i> and formed a sister group. <i>R. unicolor</i>, both trees showed strong support for its placement within a clade that included <i>Rusa</i> species and <i>R. unicolor</i> subspecies<i>.</i> The divergence times estimation analysis exhibited that the <i>A. axis</i> and <i>A. porcinus</i> divergence occurred around 3.38 MYA, suggesting a split during the late Miocene to early Pliocene. The clade containing <i>R. unicolor</i> (including <i>R. unicolor</i> subspecies) diverged approximately 3.7 MYA. These results suggested a relatively recent divergence, indicating ongoing speciation events within this group. In summary, our findings provide a new perspective on understanding <i>Axis</i> and <i>Rusa</i> species, which will not only be beneficial for species conservation but also open up new possibilities for forensic analysis.</p>

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Complete mitochondrial genomes of Axis axis and Rusa unicolor from Tamil Nadu, India and comprehensive analysis with other Cervidae

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月30日

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  • Ramesh Karunyaa,
  • Carlton Ranjith Wilson Alphonse ,
  • Babu Divya Bharathi,
  • Kalaiyarasan Boopathy Thiyagarajan,
  • Chandrasekaran Bala Amarnath,
  • Ramu Silambarasan,
  • Ashokan Jagadeesh,
  • M. G. Ganesan,
  • A. Udhayan

摘要

In India, the sambardeer (Rusa unicolor), barking deer ( Muntiacus muntjak), spotted deer (Axis axis), and Indian mouse deer (Moschiola indica, Artiodactyla: Tragulidae) are widely distributed. Deer are often poached for bush meat, skin, antlers and other purposes. The mitochondrial genome is essential for species identification and understanding evolutionary relationships. Therefore, sequencing the complete mitochondrial genome of deer species is vital for rapid species identification and conservation efforts. This study aimed to sequence the complete mitochondrial genomes of spotted and sambar deer using Next-Generation Sequencing technology. The results revealed the size of the complete mitochondrial genome (mt-DNA) of spotted deer (16,351 bp) and sambar deer (16,476 bp), respectively. Each mt-DNA encompassed 37 genes viz 13 Protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. The comparative analysis of mitochondrial nucleotide composition between Axis and Rusa species revealed closely similar ratios of A + T and G + C. Two complementary approaches (Maximum Likelihood and Bayesian Inference) were used to understand the phylogenetic relationship among Cervidae. The results indicated that the A. axis consistently formed a well-supported clade with bootstrap values of 100 and posterior probabilities of 1.000, which were closely related to A. porcinus and formed a sister group. R. unicolor, both trees showed strong support for its placement within a clade that included Rusa species and R. unicolor subspecies. The divergence times estimation analysis exhibited that the A. axis and A. porcinus divergence occurred around 3.38 MYA, suggesting a split during the late Miocene to early Pliocene. The clade containing R. unicolor (including R. unicolor subspecies) diverged approximately 3.7 MYA. These results suggested a relatively recent divergence, indicating ongoing speciation events within this group. In summary, our findings provide a new perspective on understanding Axis and Rusa species, which will not only be beneficial for species conservation but also open up new possibilities for forensic analysis.