Two complete mitochondrial genomes of the family Paradoxosomatidae (Diplopoda, Polydesmida) with phylogenetic implications

Millipedes (class Diplopoda) are vital soil invertebrates that play key roles in litter decomposition and nutrient cycling. However, their phylogenetic relationships remain poorly resolved due to limited genomic resources. In this study, we sequenced and characterized the complete mitochondrial genomes (mitogenomes) of two paradoxosomatid millipedes, <i>Oxidus gracilis</i> (15,034 bp) and <i>Kronopolites swinhoei</i> (15,277 bp). Both mitogenomes contain the typical set of 37 genes, all located on the minor strand (N-strand), and display high AT content. The conserved gene arrangement observed here may represent a molecular synapomorphy for this taxonomic group. Analysis of codon usage revealed that start codons includ ATN (ATA/ATG/ATT), TTG, and GTG, while stop codons consisted of TAN (TAA/TAG/TAT) and an incomplete single T. Relative synonymous codon usage (RSCU) analysis indicated that Leu2, Val, and Gly were the most frequently used codon families, whereas Gln, Cys, and Lys were the least utilized. The tRNA genes formed two distinct clusters, and the rRNAs were flanked by tRNA-Val. The D-loop region was located in a similar position in both species. Phylogenetic reconstruction based on 13 protein-coding genes from 34 diplopod species, using both Bayesian inference and maximum likelihood methods, strongly supported the interordinal relationships among Julida, Spirostreptida, and Spirobolida, and placed <i>O. gracilis</i> and <i>K. swinhoei</i> in distinct clades. Our findings provide valuable mitogenomic data and new phylogenetic insights into Diplopoda, underscoring the importance of expanded taxonomic sampling to further elucidate evolutionary relationships within this ecologically significant group.