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

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.

本研究对粪栖寄生螨（Parasitus fimetorum）的线粒体基因组（mitochondrial genome）进行测序，旨在探究寄螨目（Parasitiformes）下寄生螨科（Parasitidae）的转运RNA（transfer RNA, tRNA）基因二级结构。研究人员借助tRNAscan-SE与ARWEN软件，鉴定并推断出粪栖寄生螨的22个tRNA基因的二级结构，并将其与已测序寄生螨科物种的22个tRNA基因进行比对。结果显示，寄生螨科的多数tRNA基因具有典型的三叶草形二级结构；折叠过程中会出现碱基替换或错配现象，且茎区的碱基变异程度低于环区，表现出较高的保守性。碱基组成呈现出明显的A+T偏好性。相对同义密码子使用偏性（Relative Synonymous Codon Usage, RSCU）分析结果表明，寄生螨科物种tRNA基因的密码子第三位偏好使用以A或U结尾的密码子。有效密码子数绘图（ENC-plot）分析显示，多数基因分布于标准曲线下方，表明寄生螨科物种的密码子使用模式更易受自然选择压力的影响。系统发育分析结果表明，寄生螨科为单系群。本研究填补了寄生螨科线粒体tRNA基因相关研究的空白，对于理解tRNA基因序列与二级结构在比较基因组学中的重要意义具有深远价值，同时为寄生螨科物种演化的后续研究提供了助力。