Comparative Mitogenomic Analysis of Three Chionea Species (Tipulomorpha: Limoniidae): Insights into Phylogenetic Relationships and Selection Pressure

<i>Chionea</i> is classified within the Tipuloidea superfamily and predominantly inhabits cold regions. However, its phylogenetic relationships remain contentious. In this study, the first three mitogenomes of <i>Chionea</i> (Diptera: Limoniidae) sampled in northeastern China (Jilin region) were sequenced, and their phylogenetic relationships were reconstructed by integrating these sequences with 30 additional Tipuloidea mitogenomes retrieved from NCBI. Unlike other Tipuloidea species, which are predominantly distributed in relatively warmer regions, this research investigates whether positive selection has acted on the mitogenomes of these three <i>Chionea</i> species due to environmental pressures, thereby elucidating key evolutionary drivers for <i>Chionea</i>. The three mitogenomes of <i>Chionea</i> exhibit characteristic features typical of insect mitogenomes, comprising 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA genes (tRNA), and a single non-coding control region (D-loop). Notably, the secondary structure of trnS1 lacks the DHU arm in all three samples, and UUA (Leu) emerges as the most frequently utilized codon. Furthermore, the <i>COX2</i> and <i>ND5</i> genes utilize incomplete stop codons "T". Utilizing these 13 PCGs, we reconstructed the internal phylogenetic relationships within Tipuloidea, revealing that <i>Chionea tianhuashana</i> and <i>C. sphaerae</i> form sister branches, while (<i>C. tianhuashana</i> + <i>C. sphaerae</i>) constitutes a sister branch to <i>C. crassipes</i>. Moreover, our analysis confirms the monophyly of Tipulidae, <i>Tipula</i>, and <i>Nephrotoma</i> as well as the polyphyly of Tipulinae, Chioneinae, and Limoniidae. In the branch site model analysis, three positively selected sites were detected when <i>Chionea</i> was designated as the foreground branches: <i>COX3</i> (at position 242), <i>ND5</i> (at position 535), and <i>ND6</i> (at position 138).