Complete mitochondrial genome of Prionailurus bengalensis (Carnivora: Felidae), a protected species in China

Abstract

The complete mitochondrial genome (mitogenome) of the leopard cat Prionailurus bengalensis in China was sequenced using the shotgun genome-skimming method. The mitogenome of P. bengalensis is totally 17,006 bp in length with a higher A + T content of 60.4% than that of G + C and consists of 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region. All the PCGs initiate with a typical ATN codon and terminate with a TAA codon except for the four PCGs (COX1, ND2, ND3, and ND4) terminating with a single T—and one gene CYT B with AGA as stop codon. Most of the tRNA genes have a clover-leaf secondary structure except for tRNAS (AGN), which loses a dihydrouridine (DHU) arm. The ML phylogenetic tree showed that P. viverrinus nested in the group of P. bengalensis individuals, which is close to the clade clustered by the two genera Otocolobus and Felis.

Prionailurus bengalensis (Carnivora: Felidae: Felinae), commonly called leopard cat, is a widespread species, and the distribution range extends throughout Southern, Eastern, and Southeast Asia, which reflects its adaptation to a broad habitat niche (Hemmer 1978; Ross et al. 2015). This species has been listed in CITES Appendix II, endangered species of the Red List of Chinese Species, and also designated as “Least Concern” ver 3.1 by IUCN (Ross et al. 2015). To date, seven complete mitochondrial genomes (mitogenomes) of P. bengalensis from South Korea, West China, and Southeast Asia were reported (Park 2011; Tan et al. 2016; Li et al. 2016). We, here, sequenced the complete mitogenome of P. bengalensis from north China and constructed its relationship with other Felinae species combined with the data from GenBank.

The muscle material was obtained from a dead adult individual of P. bengalensis that was killed by poachers and captured by the forest police at the Manghe National Nature Reserve (112°38′37″E, 35°25′21″N), at the animal herbarium of which the specimen was stored (Voucher No. MB-2018M02). We sequenced the mitogenome of P. bengalensis by the shotgun genome-skimming method on an Illumina HiSeq 4000 platform (Zimmer and Wen 2015) and assembled and annotated within Geneious v11.0.3 using the complete mitogenomes of P. bengalensis from GenBank as the references. We also performed de novo assembly using SPAdes v. 3.7.1 (Bankevich et al. 2012).

The complete mitogenome of P. bengalensis is a circular-closed molecule with 17,006 bp in length (GenBank Accession No. MN121632) and consists of 13 protein-coding genes (PCGs; COX1-3, ND1-6, ND4L, ATP6, ATP8, and CYT B), two rRNAs (12S and 16S rRNA), 22 tRNAs, and one non-coding region. Most of the mitochondrial genes are encoded on the H-strand except for one PCG (ND6) and eight tRNA genes (tRNA-Gln, tRNA-Asn, tRNA-Ser, tRNA-Glu, tRNA-Ala, tRNA-Pro, tRNA-Tyr, and tRNA-Cys) on L-strand. The nucleotide composition of the whole mitogenome is 33.0% A, 26.0% C, 13.6% G, and 27.4% T with a higher A + T content (60.4%) than that of G + C (39.6%). All the PCGs initiate with a typical ATG codon expect for ND2 stating with ATC, and both ND3 and ND5 with ATA. Eight PCGs have a typical TAA termination codon, whereas others terminate with a single T—(COX 3, and ND2, ND4), TA– (ND3), or AGA (CYT B), respectively. We predicted the secondary structure of tRNAs using tRNAscan-SE (Lowe and Chan 2016) and found that 21 tRNA genes had a clover-leaf secondary structure, whereas tRNAS (AGN) lost a dihydrouridine (DHU) arm.

We constructed the phylogenetic relationship of leopard cat with other Felinae species using RAxML program with GTRGAMMA model and 1000 bootstrap replicates (Stamatakis 2014). The phylogenetic tree showed that the species Prionailurus viverrinus nested in the group of P. bengalensis individuals, which is close to the clade clustered by the two genera Otocolobus and Felis (Figure 1). It is necessary to further examine the monophyly of P. bengalensis and taxonomy of the species P. viverrinus using more samples and/or morphological and molecular data.

Figure 1.

Phylogenetic tree of Prionailurus bengalensis and other Felinae species based on 13 protein-coding genes using RAxML program with Panthera tigris and Neofelis nebulosi as outgroups. Numbers associated with branches are BS >70% and “*” represents nodes with 100% BS.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.