Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians

Shantanu Kundu,Devkant Singha,Kaomud Tyagi,Avas Pakrashi,Chinnadurai Venkatraman,Vikas Kumar,Dhriti Banerjee,Manokaran Kamalakannan

doi:10.1038/s41598-022-04907-7

Shantanu Kundu, Devkant Singha + Show 6 more

Open Access

https://doi.org/10.1038/s41598-022-04907-7

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Journal: Scientific Reports	Publication Date: Jan 18, 2022
Citations: 2	License type: open-access

Affiliation: Zoological Survey of India

Abstract

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Highlights

The world treeshrew account for 23 species under four genera (Anathana, Dendrogale, Ptilocercus and Tupaia) of two families (Tupaiidae and Ptilocercidae) which are distributed in South Asia, Southeast Asia, and Southwest China[1,2]
The mitogenome (17,164 bp) of the endangered Nicobar treeshrew, T. nicobarica was determined in the present study
Nine genes were placed on the negative strand, while the remaining 28 genes were placed on the positive strand (Table 1, Fig. 1)

Summary

Introduction

The world treeshrew account for 23 species under four genera (Anathana, Dendrogale, Ptilocercus and Tupaia) of two families (Tupaiidae and Ptilocercidae) which are distributed in South Asia, Southeast Asia, and Southwest China[1,2]. The phylogenetic analyses and divergence time were estimated to infer the evolutionary relationship of T. nicobarica comparing with other Tupaiidae species. On the basis of taxonomic classification, the mitogenomes of five Tupaiidae species were downloaded from GenBank and merged in the dataset for comparative analysis (Supplementary Table S1).

Results

Conclusion