Vol.:(0123456789) 1 3 Molecular Biology Reports https://doi.org/10.1007/s11033-021-06165-8 SHORT COMMUNICATION Sequencing and annotation of the endangered wild bufalo (Bubalus arnee) mitogenome for taxonomic assessment Ankit Shankar Pacha 1  · Parag Nigam 1  · Bivash Pandav 1  · Samrat Mondol 1 Received: 28 May 2020 / Accepted: 15 January 2021 © The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021 Abstract The wild water bufalo (Bubalus arnee) is one of the most endangered and least studied large bovid in the Indian subcon- tinent. India retains 90% of the estimated global population of >4000 individuals as two fragmented populations in Assam and Chhattisgarh, both threatened by habitat loss and degradation, hunting, disease from livestock, and hybridization with the domestic bufalos. Small, fragmented population size and potential hybridisation pressures from co-occurring domestic bufalos are the major conservation challenges. For the frst time, we sequenced the 16,357 bp long mitogenome of three opportunistically collected wild water bufalo samples from Assam (n = 1) and Chhattishgarh (n = 2). The annotated sequence has a base composition of 26.4% T, 26.6% C, 33.1% A and 13.9% G depicting an AT-rich mitogenome composition, including 13 protein-coding genes (11,361 bp), 22 transfer RNA (tRNA) (1514 bp), two ribosomal genes (2525 bp), and a non-coding control region (928 bp). The gene order is conserved with other bovid species. Comparative mitogenome analyses showed both populations are genetically similar but signifcantly diferent from domestic bufalo. We also identifed structural dif- ferences in seven tRNA secondary structures between both species. The genetic distance between wild bufalo and other bovids varied between 0.103 and 0.122. Multiple Bayesian phylogenetic trees showed that both wild and domestic water bufalo formed sister clades which were paraphyletic to other potentially sympatric species of genus Bos. This study provides baseline information on wild bufalo mitogenome for further research on phylogeny, phylogeography and hybrid assessment and help conserving this endangered species. Keyword Complete mitochondrial genome · Bubalus arnee · Bovidae · Large herbivore conservation · Endangered species Introduction The wild water bufalo (Bubalus arnee) is one of the larg- est and most endangered members of family Bovidae in the Indian subcontinent [1]. Historically distributed across Europe to South and Southeast Asia, they are currently restricted to India, Nepal, Bhutan, Thailand, Cambodia and Myanmar [2]. The species is regionally extinct from Bangla- desh, Indonesia, peninsular Malaysia, Sri Lanka, Viet Nam, Sumatra, Java and Borneo [2, 3]. With an estimated global current population size of <4000 individuals (>2500 mature individuals) and a range-wide declining population trend [2], they are considered as ‘Endangered’ by IUCN and in Appendix I of CITES [2]. The long-term viability of this species is under serious threat from habitat loss and deg- radation, hunting, disease from livestock and hybridisation with the domestic bufalos [4]. India retains more than 90% (~3500–3700 individuals) of the global wild water bufalo population, mostly distributed as fragmented populations in two states: Assam and Chhattisgarh [5]. Majority of the population is found in the northeastern state of Assam (~3000–3500 individuals) within Kaziranga National Park, Manas National Park, Dibru-Saikhowa Wildlife Sanctuary and few other areas, with a potentially small population in Meghalaya [2]. The central Indian population in the state of Chhattisgarh are clustered across a few protected areas: Udanti Wildlife Sanctuary, Bhairamgarh Sanctuary, Pamed Wildlife Sanctuary and Indravati National Park, where ~50–70 individuals are found [1]. It is listed under the Schedule I (highest level of protection) of Wildlife Protec- tion Act of India (1972). However, the fragmented nature of the populations and potential hybridisation pressures from * Samrat Mondol samrat@wii.gov.in 1 Wildlife Institute of India, Chandrabani, Dehradun 248001, India