Complete mitogenome of Kashmir musk deer ( Moschus cupreus ) and its comparative phylogenetic relationships
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ORIGINAL ARTICLE
Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships Bhim Singh1 · Kumudani Bala Gautam1 · Subhashree Sahoo1 · Ajit Kumar1 · Sandeep Kumar Gupta1 Received: 1 September 2020 / Accepted: 11 November 2020 © Springer Nature B.V. 2020
Abstract Kashmir musk deer, Moschus cupreus (KMD) is one the most threatened species endemic to the Himalayan region of Kashmir, Pakistan and Afghanistan. Herein, we have sequenced, annotated and characterized the complete mitogenome of M. cupreus. The investigation and comparison of the mitogenome provide crucial information for phylogenetic analysis to understand the evolutionary relationships. The mitogenome of KMD was 16,354 bp long, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. Its composition was highly A+T biased 68.42%, and exhibited a positive AT–skew (0.082) and negative GC–skew (− 0.307). The phylogenetic analysis suggested that KMD was a primitive and extant species in the genus Moschus, whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) were the closest relatives. It indicated the placement of M. cupreus within the monotypic family Moschidae of musk deer. Hence, it provides a better understanding of lineage identification and musk deer evolution for further research. Keywords Moschidae · Moschus cupreus · Maternal lineage phylogenetics
Introduction The Kashmir musk deer, Moschus cupreus (KMD) is a member of genus Moschus in the monotypic family Moschidae [1]. The species are endemic to the Palearctic region and mostly inhabit high altitudinal mountainous regions of the Himalayan ranges [1]. According to the IUCN database, the current population is in decline due to overexploitation, primarily caused by habitat destruction and illegal hunting of musk pod and skin in the wildlife trade. The IUCN Red List includes M. cupreus in the ‘Endangered’ category and has listed in Appendix I under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). In India, musk deer is categorized under Schedule I of the Indian Wildlife (Protection) Act, 1972. Due to limited Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-06002-4) contains supplementary material, which is available to authorized users. * Sandeep Kumar Gupta [email protected]; [email protected] 1
Wildlife Institute of India, Chandrabani, Dehra Dun, U.K. 248 001, India
ecological and genetic evidence, the distribution range and evolutionary history of the extant species of musk deers are still unclear [2]. According to Grubb 2005 [3], the distribution of M. cupreus was restricted to the Himalayan region of Kashmir, Pakistan and Afghanistan. However, a recent molecular study has provided a new distribution record of M. cupreus from Mustang, Nepal and west of Annapurna Himalayas range [4]. The availability of complete mitogenomes will furnish mo
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