The Complete Maternally and Paternally Inherited Mitochondrial Genomes of the Endangered Freshwater Mussel <i>Solenaia carinatus</i> (Bivalvia: Unionidae) and Implications for Unionidae Taxonomy

<div><p>Doubly uniparental inheritance (DUI) is an exception to the typical maternal inheritance of mitochondrial (mt) DNA in Metazoa, and found only in some bivalves. In species with DUI, there are two highly divergent gender-associated mt genomes: maternal (F) and paternal (M), which transmit independently and show different tissue localization. <i>Solenaia carinatus</i> is an endangered freshwater mussel species exclusive to Poyang Lake basin, China. Anthropogenic events in the watershed greatly threaten the survival of this species. Nevertheless, the taxonomy of <i>S. carinatus</i> based on shell morphology is confusing, and the subfamilial placement of the genus <i>Solenaia</i> remains unclear. In order to clarify the taxonomic status and discuss the phylogenetic implications of family Unionidae, the entire F and M mt genomes of <i>S. carinatus</i> were sequenced and compared with the mt genomes of diverse freshwater mussel species. The complete F and M mt genomes of <i>S. carinatus</i> are 16716 bp and 17102 bp in size, respectively. The F and M mt genomes of <i>S. carinatus</i> diverge by about 40% in nucleotide sequence and 48% in amino acid sequence. Compared to F counterparts, the M genome shows a more compact structure. Different gene arrangements are found in these two gender-associated mt genomes. Among these, the F genome <i>cox2-rrnS</i> gene order is considered to be a genome-level synapomorphy for female lineage of the subfamily Gonideinae. From maternal and paternal mtDNA perspectives, the phylogenetic analyses of Unionoida indicate that <i>S. carinatus</i> belongs to Gonideinae. The F and M clades in freshwater mussels are reciprocal monophyly. The phylogenetic trees advocate the classification of sampled Unionidae species into four subfamilies: Gonideinae, Ambleminae, Anodontinae, and Unioninae, which is supported by the morphological characteristics of glochidia. </p>