Comparative analysis of mitogenomes in six Scolopendra species (Chilopoda, Scolopendromorpha): insights into rare genetic rearrangements and phylogeny

Six complete mitochondrial genomes from species within <i>Scolopendra</i> (Scolopendromorpha) (<i>S.alcyona</i>, <i>S.calcarata</i>, <i>S.cataracta</i>, <i>S.lufengia</i>, <i>S.mazbii</i>, and <i>S.multidens</i>) were analyzed. The mitochondrial genomes ranged in size from 14,422 bp to 15,458 bp, with A+T content varying between 67.00% and 74.53%. All PCGs and rRNA were successfully identified, though tRNAs exhibited widespread loss. Additionally, supplementary control region sequences were identified in three species. Beyond sequence data, the arrangement of mitochondrial genes can provide additional phylogenetically relevant information. The mitogenome arrangements in <i>S.alcyona</i>, <i>S.cataracta</i>, <i>S.lufengia</i>, and <i>S.mazbii</i> are consistent with the inferred ancestral arrangement in Myriapoda, but <i>Scolopendramultidens</i> had a duplication of tRNA and <i>S.calcarata</i> underwent a significant gene rearrangement. The Tandem Duplication/Random Loss model and tRNA mispriming mode were determined as most likely explanations for the observed gene rearrangements. Phylogenetic trees were reconstructed using the six newly sequenced mitogenomes and published mitochondrial data from other Chilopoda species. The results revealed two major monophyletic clades within <i>Scolopendra</i>: one comprising <i>S.alcyona</i>, <i>S.dehaani</i>, <i>S.cataracta</i>, <i>S.lufengia</i>, <i>S.morsitans</i>, <i>S.multidens</i>, and <i>S.mutilans</i>, and the other uniting <i>S.mazbii</i> and <i>S.calcarata</i>. Notably, <i>S.subspinipes</i> unexpectedly clustered with <i>Scolopocryptops</i> sp., challenging the monophyly of <i>Scolopendra</i> and highlighting the need for revised taxonomic evaluations. These results enhance our understanding of gene rearrangements and evolutionary dynamics in Scolopendromorpha, offering critical insights into their phylogenetic relationships.