Characterization and phylogenetic analysis of the complete mitochondrial genome of Rhabdias kafunata (Rhabditida: Rhabdiasidae)

Abstract

Rhabdias kafunata (Rhabditida: Rhabdiasidae) is a parasitic nematode that significantly affects bufonids. To better understand the genome-level characteristics of related species, Illumina sequencing was used to identify mitochondrial genes and analyze their basic characteristics and gene arrangements. The mitogenome of R. kafunata is 14,068 bp in length and contains 36 genes, including 12 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one noncoding region (NCR). The nucleotide composition is highly biased toward A + T, accounting for 75.5% of the entire mitochondrial genome. The cox1 sequence is relatively conserved in Ka/Ks analyses and can be used as a gene fragment for species identification. While 8 of the 12 PCGs use the typical ATN initiation codon, nad1-2, nad4, and cox3 utilize a TTG initiation codon. Most stop codons end with the standard TAA or TAG, except for cytb, which ends with an incomplete TA. Additionally, trnM, trnK, and trnI have the typical clover-leaf secondary structure, while the remaining tRNAs lack the DHU arm or TΨC arm. Phylogenetic analysis indicates that R. kafunata belongs to the Rhabditidae family and is closely related to Litoditis marina and Caenorhabditis angaria among sequenced lepidopteran mitochondrial genomes.