| Summary: | <p><strong>Background:</strong> The Mephitidae is a family of skunks and stink-badgers that includes 12 extant
species in four genera namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only
genus within Mephitidae found outside the American continent, with its distribution limited to
the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e.
javanensis and marchei. Currently, complete mitogenomes are unavailable for either species.
Here, we present the characterization of the first complete mitogenome for the Sunda stinkbadger (Mydaus javanensis) from the island of Borneo.</p>
<p><strong>Methods:</strong> Muscle tissue was obtained and the DNA was sequenced using a combination of
Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome
was annotated with MITOS and manually checked for accuracy. A circular map of the
mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and
codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were
aligned with reference sequences from GenBank and used for the construction of phylogenetic
trees (ML and BI). Additionally, due to the lack of available complete genomes in public
databases, we constructed another tree with the cyt b gene.</p>
<p><strong>Results:</strong> The complete circular mitogenome was 16,391 base pairs in length. It comprises the
typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR)
and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A
and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with
five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional
polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most
common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI
phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly
clustered the species with other members of the Mephitidae family but were unique enough to set
it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the
mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the
species.</p>
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