The first complete mitochondrial genome of Sumatran striped rabbit Nesolagus netscheri (Schlegel, 1880), and its phylogenetic relationship with other Leporidae

Abstract

Nesolagus netscheri, a Sumatran striped rabbit, is one of the rarest rabbits in the Leporidae family, and its genetic information is still limited. This study provides the first mitochondrial genome and molecular systematic characterization of the Sumatran striped rabbit, Nesolagus netscheri, Indonesia's rarest rabbit. It consists of a circular double-stranded DNA of 16,709 bp. It showed that the mitochondrial genome structure of N. netscheri is similar to that of N. timminsi. The mitochondrial genome of N. netscheri contained 22 transfer RNA (tRNA) genes, and all tRNA except for trnS1 showed a characteristic cloverleaf secondary structure. Evidence was found that the atp8 gene of N. netscheri is under positive selection pressure. The phylogenetic analysis shows Leporidae was monophyletic, with Nesolagus at the basal. The study indicates a split between N. netscheri and N. timminsi in the Late Pleistocene around 0.43 million years ago. This research is a fundamental reference for the conservation of the rarest lagomorph species and provides important information for future evolutionary studies in the Leporidae family.

Keywords: Leporidae; Mitochondrial genome; Phylogenetic; Sumatran striped rabbit (Nesolagus netscheri).

Fig. 1

(a) Circular representation of the mitochondrial genome of Nesolagus netscheri. The colored blocks indicate different gene types, with genes encoded on the light and heavy strands in counterclockwise and clockwise orientations, respectively. The black inner circle represents the GC content of the mitogenome, while the pink and red regions indicate GC skew. The rabbit illustration was adapted from https://scentsindonesia.com; (b) Geographic distribution of N. netscheri (orange regions) within its habitat. The map was created using QGIS version 3.40.1 Bratislava (https://www.qgis.org).

Fig. 2

Relative synonymous codon usage (left) and codon distribution (right) in the mitochondrial protein-coding genes of N. netscheri.

Fig. 3

Secondary structure of tRNAs in the mitochondrial genome of N. netscheri.

Fig. 4

Selective pressure analysis of the protein-coding genes (PCGs) of N. netscheri. By employing two distinct leporid mitogenomes as references, the Ka/Ks ratios were determined for each of the 13 PCGs.

Fig. 5

The phylogenetic tree of Leporidae is based on 13 PCGs (11,396 bp), which is estimated using the Bayesian relaxed-molecular clock method. Posterior probability values from Bayesian inference and percentages of bootstrap from maximum likelihood analyses are listed on each node, respectively. Purple bars were used to show the 95% HPD for each node, with each genus represented by a different color.