A Novel Clonorchis sinensis Mitogenome: Elucidating Multiregional Strain Phylogeny and Revising the Digenean Mitochondrial Genome Tree

<i>Clonorchis sinensis</i>, a parasitic liver fluke, is the primary aetiological agent of clonorchiasis, a disease predominantly characterized by liver-related clinical manifestations. Currently, research on the complete mitochondrial (mt) genome of local <i>C. sinensis</i> populations remains inadequate. Thus, in this study, we sequenced and annotated the mt genome of fish-borne <i>C. sinensis</i> (Cs-c2) from Changchun, Jilin Province, China, a strain not previously described. This mt genome is 14,136 bp in length and harbours 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a single control region (CR). We constructed a maximum likelihood (ML) phylogenetic tree using concatenated <i>ND5</i>, <i>ND6</i>, and <i>ND1</i> from protein-coding genes (PCGs) of the <i>C. sinensis</i> mitochondrial genome (mt genome). This tree more clearly differentiated <i>C. sinensis</i> strains from three geographical regions (China, Russia, and South Korea) and distinguished Opisthorchiidae from two closely related families (Fasciolidae and Dicrocoeliidae). Additionally, we constructed an ML phylogenetic tree using concatenated <i>ND4</i>, <i>ND5</i>, <i>ND1</i>, <i>ND2</i>, and <i>COX1</i> from the PCGs of digenean (Digenea) mt genomes. This approach-utilizing multiple high-resolution PCGs with evolutionary rates distinct from those of the mt genome-yielded robust clustering for multiple suborders and 13 families within Digenea and provided new molecular evidence for intergeneric relationships within the suborder Plagiorchiata of Digenea. These findings serve as important references for future research on the differentiation of closely related geographical strains of digeneans, as well as for studies on molecular taxonomy and population genetics.