Comparative analysis of tRNA genes in the mitochondrial genome of Parasitidae (Parasitiformes: Mesostigmata)

ABSTRACT The mitochondrial genome of Parasitus fimetorum was sequenced to study the Parasitidae tRNA gene secondary structure in Parasitiformes. tRNAscan-SE and ARWEN identified and inferred the secondary structures of 22 tRNA genes of Parasitus fimetorum, which were compared to 22 tRNA genes in sequenced Parasitidae mitochondrial genomes. The results showed that most tRNA genes of Parasitidae had a typical cloverleaf secondary structure; the base substitutions or mismatches occurred during the folding process, and the stem region showed less base variation than the loop region, showing high conservation. The base composition showed a clear preference for A + T. Relative synonymous codon usage (RSCU) analysis showed that the third codon of tRNA genes in Parasitidae species preferred to use codons that ended with A or U. ENC-plot analysis showed that most genes were distributed under the standard curve, indicating that codon usage in Parasitidae species was more influenced by natural selection pressure. Phylogenetic analysis showed that Parasitidae is a monophyletic group. This study complements the research on mitochondrial tRNA genes in Parasitidae, which has far-reaching implications for understanding the importance of tRNA gene sequences and secondary structures in comparative genomics and facilitates further studies on the evolution of species in the Parasitidae.