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Background <p><i>Arunachali</i> yak is the first registered yak breed of India and is mainly distributed in the Tawang and West Kameng districts of Arunachal Pradesh. Despite its socio-economic importance, complete mitochondrial genomic information for this breed has remained unavailable. The present study aimed to characterize the complete mitochondrial genome and infer the phylogenetic relationship of <i>Arunachali</i> yak with other bovids.</p> Methods and Results <p>High-quality genomic DNA isolated from <i>Arunachali</i> yak blood was sequenced using the PacBio Sequel II long-read platform. The complete mitochondrial genome was assembled as a circular double-stranded molecule of 16,324 bp comprising 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and an 894 bp control region (D-loop). The mitogenome exhibited AT-rich nucleotide composition with positive AT skew and negative GC skew. Relative synonymous codon usage analysis showed preference for codons ending with A or T at the third codon position. Ka/Ks ratios of all protein-coding genes were &lt;1, indicating strong purifying selection. Phylogenetic analyses using Maximum Likelihood and Bayesian Inference methods produced congruent topologies and clustered <i>Arunachali</i> yak with other domestic yak breeds and wild yak (<i>Bos mutus</i>) within a single monophyletic clade. <i>Arunachali</i> yak showed close maternal affinity with Gannan yak and was positioned within the mt-I yak lineage.</p> Conclusions <p>This study presents the first complete mitochondrial genome characterization of <i>Arunachali</i> yak and provides new insights into its mitochondrial genome organization and phylogenetic relationships with other bovids. The generated mitogenome represents an important genetic resource for future phylogenetic, comparative genomic, and biodiversity conservation studies in yak populations.</p>

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De novo mitogenome assembly and phylogenetic implications of the first Indian yak breed-Arunachali (Bos or Poephagus grunniens L.)

  • 期刊论文

  • 发表日期：

    2026年6月30日

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  • Martina Pukhrambam,
  • Pranab J. Das,
  • Kishor U. Tribhuvan,
  • Atrayee Dutta,
  • Mihir Sarkar

摘要

Background

Arunachali yak is the first registered yak breed of India and is mainly distributed in the Tawang and West Kameng districts of Arunachal Pradesh. Despite its socio-economic importance, complete mitochondrial genomic information for this breed has remained unavailable. The present study aimed to characterize the complete mitochondrial genome and infer the phylogenetic relationship of Arunachali yak with other bovids.

Methods and Results

High-quality genomic DNA isolated from Arunachali yak blood was sequenced using the PacBio Sequel II long-read platform. The complete mitochondrial genome was assembled as a circular double-stranded molecule of 16,324 bp comprising 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and an 894 bp control region (D-loop). The mitogenome exhibited AT-rich nucleotide composition with positive AT skew and negative GC skew. Relative synonymous codon usage analysis showed preference for codons ending with A or T at the third codon position. Ka/Ks ratios of all protein-coding genes were <1, indicating strong purifying selection. Phylogenetic analyses using Maximum Likelihood and Bayesian Inference methods produced congruent topologies and clustered Arunachali yak with other domestic yak breeds and wild yak (Bos mutus) within a single monophyletic clade. Arunachali yak showed close maternal affinity with Gannan yak and was positioned within the mt-I yak lineage.

Conclusions

This study presents the first complete mitochondrial genome characterization of Arunachali yak and provides new insights into its mitochondrial genome organization and phylogenetic relationships with other bovids. The generated mitogenome represents an important genetic resource for future phylogenetic, comparative genomic, and biodiversity conservation studies in yak populations.