Comparative mitogenomic analysis and phylogeny of Veneridae with doubly uniparental inheritance

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.