The complete mitochondrial genome and phylogenetic analysis of red-and-white giant flying squirrel (Petaurista alborufus)

Abstract

Red-and-white giant flying squirrel (Petaurista alborufus) is a widely distributed but rarely studied species. Here, we sequenced the complete mitochondrial genome about it, which is a circular genome of 16,511 bp and have a typical structure with mammals. The base composition shows higher composition of A\T. There are 61 variations and eight base deletions between two sequences when compared with the reported sequence (JQ743657). In this study, we obtain a new mitochondrial genome sequence of red-and-white giant flying squirrel, which provide novel molecular information that could prove fundamental to our understanding of diversity research and phylogenetic structure.

Red-and-white giant flying squirrel (Petaurista alborufus), a nocturnal arboreal small mammals, lives in a variety of habitat such as dense forest, limestone cliffs, and Taiwan hardwood with an elevation of 800–3500 m in Taiwan, the southwest of China and Burma (Lee et al. 1993; IUCN 2008; Smith and Xie 2008; Kuo and Lee 2012). For the species, hunting may be a threat that it is a major game species (Lee et al. 1993). Moreover, we have a limited knowledge about it and less understanding of phylogenetic history because of no data about population status of this species and less genetic diversity research, and there only two complete mitochondrial genome were recorded (Oshida et al. 2000; Xu et al. 2019). Here, we obtained a sample of muscle of red-and-white giant flying squirrel, which from Xishui county (N 28°33′, E 106°2′), Guizhou, China and was stored in Museum of Sichuan Agricultural University (Accession: 000751) and sequenced the complete mitochondrial genome, in order to provide more useful molecular information about diversity research and analyze the phylogenetic structure.

We got total genomic DNA that was extracted by proteinase K digestion, phenol, and chloroform extraction (Deininger 1990). The reference sequence (JQ743657) was available for download in the Genbank. Based on this, we designed 22 pairs of primer and mitochondrial genome of Red-and-white Giant Flying Squirrel was successfully amplified. We blast the sequence in the National Center for Biotechnology Information (NCBI); it shows 99% similarity with reference sequence.

The complete mitochondrial genome of red-and-white giant flying squirrel is 16,511 bp (Genbank number MN011572), the genome contains two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes (PCGs), and one control region (D-loop) that was same as most vertebrate (Roos 2018; Wu et al. 2018). All of these genes are encoded on H-strand except for ND6 and eight tRNA genes on L-strand. The majority initiation codon of PCGs is ATG, but ND3 and ND5 is ATA, ND2 is ATC. About the termination codon, Six PCGs use TAA, cytochrome b (Cytb) use ATA, ND6 use AGG, whereas the other five genes end with TA– or T––. These incomplete termination codons may be accomplished by post-transcriptional polyadenylation (Kong et al. 2015). The base composition of red-and-white giant flying squirrel is A: 31.78% T: 28.5% C: 26.5% G: 13.22% and the A + T = 60.28%, C + G = 39.72%, it shows obvious preference of A\T. There are 61 variations and eight base deletions when compared with the reported sequence (JQ743657).

To further explore its taxonomic status and phylogenetic analysis, a maximum-likelihood (ML) phylogenetic tree (Figure 1) that included 16 species complete mitochondrial genome of sciuridae and two outgroups (Apodemus draco and Cricetulus migratorius) was constructed in MEGA10.0 (Kumar et al. 2018). In the ML phylogenetic tree, 16 species of sciuridae were classified into one large clade, and two outgroups were classified another clade, which supported the taxonomic status of our samples. The research is expected to contribute to molecular identification and phylogenetic analysis of P. alborufus.

Figure 1.

Maximum-likelihood tree of red-and-white giant flying squirrel (Petaurista alborufus) with other 16 sequences from sciuridae species and two outgruops. Numbers on nodes refer to bootstrap values and GenBank accession numbers are listed below species. Petaurista alborufus represented a sequence in this study.

Funding Statement

This work was supported by the National Natural Science Foundation of China under Grant [31370407].

Disclosure statement

The authors declare no conflicts of interest and are alone responsible for the content and writing of the paper.