Doubly uniparental inheritance (DUI) is an atypical animal mtDNA inheritance system, reported so far only in bivalve species, in which two mitochondrial lineages exist: one transmitted through the egg (F-type) and the other through the sperm (M-type). Although numerous species exhibit this unusual organelle inheritance, it is primarily documented in marine and freshwater mussels. The distribution, function and molecular evolutionary implications of DUI in the family Veneridae, however, remain unclear. Here, we investigated 17 species of Veneridae, compared mitochondrial genomes of DUI species and reconstructed their phylogenetic framework. Different sex-linked mitochondrial genomes have been identified in the male gonads and adductor muscles of 7 venerids, indicating the presence of DUI in these species. Analysis of the unassigned regions (URs) of the mitochondrial genome in DUI species revealed that 13 out of 44 URs contained repetitive sequences, with nine being long unassigned regions (LURs). All LURs were capable of forming secondary structures, and most of them exhibited patterns of significant sequence similarity to elements known to have specific functions in the control regions of sea urchins and mammals. The F/M phylogeny showed that DUI venerids exhibit both taxon-specific patterns and gender-specific patterns, with Gafrarium dispar experiencing masculinization events.

Most recently, species identification has leaped from DNA barcoding into shotgun sequencing-based “genome skimming” alternatives. Genome skims have mainly been used to assemble organelle genomes, which discards much of the nuclear genome. Recently, an alternative approach was proposed for sample identification, using unassembled genome skims, which can effectively improve phylogenetic signal and identification resolution. Studies have shown that the software Skmer and APPLES work well at estimating genomic distance and performing phylogenetic placement in birds and insects using low-coverage genome skims. In this study, we use Skmer and APPLES based on genome skims of 11 patellogastropods to perform assembly-free and alignment-free species identification and phylogenetic placement. Whether or not data corresponding to query species are present in the reference database, Skmer selects the best matching or closest species with COI barcodes under different sizes of genome skims except lacking species belonging to the same family as a query. APPLES cannot place patellogastropods in the correct phylogenetic position when the reference database is sparse. Our study represents the first attempt at assembly-free and alignment-free species identification of marine mollusks using genome skims, demonstrating its feasibility for patellogastropod species identification and flanking the necessity of establishing a database to share genome skims.

The superfamily Tellinoidea is one of the most diverse groups of marine bivalves, with significant ecological and economic value. To date, the availability of complete mitochondrial genome data within Tellinoidea remains limited, and the taxonomic coverage is still insufficient to resolve its internal controversies. The current study aims to further explore the phylogenetic relationships within Tellinoidea through denser sampling. We have newly sequenced the mitochondrial genomes of 13 species, among which seven genera are being published for the first time. Combined with the published mitogenomes and transcriptomic data, we constructed the most comprehensive Tellinoidea phylogeny to date through maximum likelihood and Bayesian Inference analyses. Our findings support the monophyly of the superfamily Tellinoidea, with Semelidae nesting as a monophyletic group within Tellinidae. We also support the paraphyly of Tellinidae based on the mitochondrial genome data for the first time, identifying that the two subfamilies (Macominae and Tellininae) are polyphyletic. Gene rearrangement analysis reveals a relatively high degree of variation in Semelidae. By expanding the mitochondrial genome dataset, this study provides new insights into the phylogeny of Tellinoidea and underscores the need for further sampling of species to reassess the phylogenetic relationships of Tellinidae and the entire Tellinoidea.