Abstract
The complete mitochondrial genome sequence of the Hylopetes alboniger was sequenced and reported for the first time using muscle tissue. The mitochondrial genome is 16,584 bp in size, including 22 tRNA genes, 13 protein-coding genes, 12S rRNA, 16S rRNA, and one control region. Phylogenetic analysis was performed using whole mitogenome sequences with other 15 closely related taxa to assess their phylogenetic relationship. This mitochondrial genome sequence will provide a better understanding for H. alboniger evolution in the future.
Keywords: Complete mitochondrial genome, arrow-tailed flying squirrel, Hylopetes alboniger
The arrow-tailed flying squirrel (Hylopetes) is a polymorphic genus and occurs in the eastern Himalayas to the Greater Sundaland. The natural habitats of Hylopetes are subtropical or tropical dry forests which are continuing to decline in extent and quality (Yu et al. 2014). More than 10 Hylopetes forms have been described as valid species in different taxonomic revisions on the basis of dental and cranial characteristics and external structures. However, recognition of some species is based on few specimens; some are based solely on skins; and some actually are synonyms or subspecies of other valid species (Thorington & Darrow 2000; Rasmussen & Thorington 2008). Therefore, it is a great significance for the identification of Hylopetes on the molecular level. In genus Hylopetes, only one complete mitochondrial genomes can be queried in National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/), namely, 16,530 bp Hylopetes phayrei KC447305. Given this, it seems particularly important to obtain the mitochondrial genome sequence of this species. We expect that this work can provide some available information for clarifying the taxonomic dispute surrounding H. alboniger.
In this study, the H. alboniger was obtained from wild field in Baima Snow Mountain, Yunnan, China (Geospatial coordinates: E 99°18′823″, N 27°35′320″, with accession No. HA-15-02, China West Normal University). We obtained the complete mitochondrial genome of H. alboniger, and submitted it into the GeneBank database with an accession number KX710106. The complete genome is 16,584 bp in size and contains 22 tRNA genes, 13 protein-coding genes (PCGs), 12S rRNA and 16S rRNA, and one control region. The base composition is: A, 32.1%; T, 30.2%; C, 24.9%; and G, 12.8%. Most PCGs are in the heavy chain except ND6. ATG is the most commonly used start codon in H. alboniger mitochondrial PCG, while ND2 start with ATA, ND3 and ND5 start with ATT. Three genes end with an incomplete stop codon TA– (COX3 and ND3) or T–– (ND4). ND2, ND6, and Cytb genes terminate with TAG, AGG, and AGA, respectively. And the other seven genes end on the usual TAA stop codons.
The mitochondrial genome has been broadly applied in population genetics and phylogenetic (Singh 2008; Galtier et al. 2009). To further validate the taxonomy and phylogenetic relationships, phylogenetic analysis was constructed by whole mitogenome sequences with 15 closely related taxa. A neighbour-joining (NJ) tree was constructed using MEGA 6 (Tamura et al. 2013) with 1000 bootstrap replicates (Figure 1). From the phylogenetic tree, we can see that H. alboniger first clustered with H. phayrei, and then together with other four species, including three Petaurista sp. (P. alborufus, P. hainana, and P. elegans caniceps), Pteromys volans and Sciurus vulgaris forming a single branch.
Figure 1.
NJ tree inferred from the nucleotide sequence of whole mitogenome. The numbers above branches specify bootsrap percentages (1000 replicates). The species were selected from P. elegans caniceps (KU579289); P. volans (JQ230001); H. phayrei (KC447305); P. alborufus (JQ743657); P. hainana (JX572159); S. vulgaris (AJ238588); D. rufigenis (KC447304); T.s swinhoei (KP027416); T. sibiricus (KF668525); Callosciurus erythraeus (KM502568); Ictidomys tridecemlineatus (KP698974); Cynomys leucurus (KP326309); C. ludovicianus (KP326310); Marmota himalayana (JX069958); Ratufa bicolor (KF575124).
Acknowledgements
We are grateful to our field assistants Shuikai Feng. We thank Baimaxueshan Nature Reserve for our work permit. Foundation of key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University.
Disclosure statement
The authors have declared no conflicting interests. The authors alone are responsible for doing the research and writing the paper.
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