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Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor)

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Abstract

Sambar (Rusa unicolor) is the largest oriental deer and has a wide distribution across South and Southeast Asia. Despite its wide distribution range, little information on the genetics of this species is available to date. We examined the genetic variability of Sambar populations using a partial fragment of the mtDNA control region and reconstructed the phylogeographic association of Sambar populations across India. We detected 56 haplotypes with an overall haplotype diversity, Hd = 0.939 ± 0.012 and nucleotide diversity, Pi = 0.029 ± 0.002 in Sambar populations across India. The Sambar populations of Northeast India exhibits 30 localized mtDNA control region haplotypes with no haplotype sharing with other populations of India. We identified a 40 bp tandem repeat motif in the mtDNA control region with variable copy numbers ranging between three to six duplications. The Sambar populations across India exhibited phylogeographic differentiation based on the observed insertion and deletion patterns in the mtDNA control region. The 40 bp tandem repeat motif was associated with patterns of insertions and deletions among different populations of Sambar in India. The findings of this study provide baseline information on the mtDNA genetic variability of Sambar populations across India, which is crucial for future population genetic studies.

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The sequence data is submitted to GenBank under Accession No. MT952164- MT952193.

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Acknowledgements

This study was conducted under the project, “Genetic Assessment of Sambar (Rusa unicolor) populations in Northeast India”, sponsored by the SERB, Department of Science and Technology, Government of India. We thank the Director and Dean, Wildlife Institute of India (WII) for their support. We are grateful to the Forest Departments of Assam, Arunachal Pradesh, Meghalaya, Manipur, Mizoram, and Nagaland States for providing research permits and logistic support for the study. We express our gratitude to the members of WFCG Cell and volunteers for their support and assistance in field surveys.

Funding

This study was conducted under the project, “Genetic Assessment of Sambar (Rusa unicolor) populations in Northeast India”, sponsored by the SERB, Department of Science and Technology, Government of India.

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Authors and Affiliations

  1. Wildlife Institute of India, Dehra Dun, Uttarakhand, 248001, India

    Mirza Ghazanfarullah Ghazi, Syed Ainul Hussain & Sandeep Kumar Gupta

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  1. Mirza Ghazanfarullah Ghazi
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  2. Syed Ainul Hussain
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  3. Sandeep Kumar Gupta
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Correspondence to Sandeep Kumar Gupta.

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Ghazi, M.G., Hussain, S.A. & Gupta, S.K. Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor). Mol Biol Rep 48, 4129–4135 (2021). https://doi.org/10.1007/s11033-021-06426-6

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  • DOI: https://doi.org/10.1007/s11033-021-06426-6

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