The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida

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.

Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts

Insect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.

A proposed method for analyzing molecular signatures to detect hermaphroditism in freshwater mussels: a case study using the eastern floater (Pyganodon cataracta)

Many freshwater mussels (order Unionida) have an unusual system of doubly uniparental inheritance (DUI) of mitochondrial (mt) DNA. In species with DUI, males possess a female-transmitted (F-type) mt genome and a male-transmitted (M-type) mt genome. These genomes contain non-canonical open reading frame (orf) genes, referred to as f-orf and m-orf, present in F and M mt genomes, respectively. These genes have been implicated in sexual development in Unionida. When gonochoric species become hermaphroditic, which has happened several times in Unionida, they lose their M-type mt genome and f-orf genes evolve dramatically. Resulting F-ORF proteins are highly divergent in terms of primary nucleotide sequence, inferred amino acids, and hydrophobic properties; these genes (and proteins) are referred to as hermaphroditic orfs or h-orfs (and H-ORFs). We investigated patterns of hydrophobicity divergence for H-ORF proteins in hermaphrodites versus F-ORF proteins in closely related gonochoric species against cytochrome c oxidase subunit 1 (cox1) divergences. This approach was used to assess whether cryptic hermaphrodites can be detected. Although we did not detect evidence for the recent transition of any populations of eastern floaters (Pyganodon cataracta (Say, 1817)) to hermaphroditism, our analyses demonstrate that molecular signatures in mtDNA can be used to detect hermaphroditism in freshwater mussels.

Bivalve molluscs as model systems for studying mitochondrial biology

The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.

Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria

In animals, strictly maternal inheritance (SMI) of mitochondria is the rule, but one exception (doubly uniparental inheritance or DUI), marked by the transmission of sex-specific mitogenomes, has been reported in bivalves. Associated with DUI is a frequent modification of the mitochondrial cox2 gene, as well as additional sex-specific mitochondrial genes not involved in oxidative phosphorylation. With the exception of freshwater mussels (for 3 families of the order Unionida), these DUI-associated features have only been shown in few species [within Mytilidae (order Mytilida) and Veneridae (order Venerida)] because of the few complete sex-specific mitogenomes published for these orders. Here, we present the complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida, Scrobicularia plana (Semelidae) and Limecola balthica (Tellinidae). These species display the largest differences in genome size between sex-specific mitotypes in DUI species (>10 kb), as well as the highest mtDNA divergences (sometimes reaching >50%). An important in-frame insertion (>3.5 kb) in the male cox2 gene is partly responsible for the differences in genome size. The S. plana cox2 gene is the largest reported so far in the Kingdom Animalia. The mitogenomes may be carrying sex-specific genes, indicating that general mitochondrial features are shared among DUI species.

Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)

BACKGROUND

Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products.

RESULTS

We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features.

CONCLUSIONS

The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.

Phylogeny of European Anodontini (Bivalvia: Unionidae) with a redescription of Anodonta exulcerata

Freshwater bivalves are highly threatened and globally declining due to multiple anthropogenic impacts, making them important conservation targets. Because conservation policies and actions generally occur at the species level, accurate species identification and delimitation is critical. A recent phylogenetic study of Italian mussel populations revalidated an Anodonta species bringing the number of known European Anodontini from three to four species. The current study contributes to the clarification of the taxonomy and systematics of European Anodontini, using a combination of molecular, morphological and anatomical data, and constructs phylogenies based on complete mitogenomes. A redescription of A. exulcerata and a comparative analysis of morphological and anatomical characters with respect to the other two species of Anodonta present in the area are provided. No reliable diagnostic character has emerged from comparative analysis of the morphometric characters of 109 specimens from 16 sites across the Italian peninsula. In fact, the discriminant analysis resulted in a greater probability of correct assignment to the site of origin than to the species. This confirms the difficulties of an uncritical application of visual characters for the delimitation of species, especially for Anodontinae.