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Background  Many species of bivalves exhibit a unique system of mtDNA transmission named Doubly Uniparental Inheritance (DUI). Under this system, species have two distinct, sex-linked mitochondrial genomes: the M-type mtDNA, which is transmitted by males to male offspring and found in spermatozoa, and the F-type mtDNA, which is transmitted by females to all offspring, and found in all tissues of females and in somatic tissues of males. Bivalves with DUI also have sex-specific mitochondrial ORFan genes, (M- orf  in the M mtDNA, F- orf  in the F mtDNA), which are open reading frames having no detectable homology and no known function. DUI ORFan proteins have previously been characterized  in silico  in a taxonomically broad array of bivalves including four mytiloid, one veneroid and one unionoid species. However, the large evolutionary distance among these taxa prevented a meaningful comparison of ORFan properties among these divergent lineages. The present  in silico  study focuses on a suite of more closely-related Unionoid freshwater mussel species to provide more reliably interpretable information on patterns of conservation and properties of DUI ORFans. Unionoid species typically have separate sexes, but hermaphroditism also occurs, and hermaphroditic species lack the M-type mtDNA and possess a highly mutated version of the F- orf  in their maternally transmitted mtDNA (named H -orf  in these taxa). In this study, H -orf s and their respective proteins are analysed for the first time.    Results  Despite a rapid rate of evolution, strong structural and functional similarities were found for M- ORF  proteins compared among species, and among the F -ORF  and H -ORF  proteins across the studied species.  In silico  analyses suggest that M- ORF s have a role in transport and cellular processes such as signalling, cell cycle and division, and cytoskeleton organisation, and that F- ORF s may be involved in cellular traffic and transport, and in immune response. H- ORF s appear to be structural glycoproteins, which may be involved in signalling, transport and transcription. Our results also support either a viral or a mitochondrial origin for the ORFans.    Conclusions  Our findings reveal striking structural and functional similarities among proteins encoded by mitochondrial ORFans in freshwater mussels, and strongly support a role for these genes in the DUI mechanism. Our analyses also support the possibility of DUI systems with elements of different sources/origins and different mechanisms of action in the distantly-related DUI taxa. Parallel situations to the novel mitochondrially-encoded functions of freshwater mussel ORFans present in some other eukaryotes are also discussed.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2986-6) contains supplementary material, which is available to authorized users.

bmc genomics

In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function