Complete sequences of mitochondrial genomes from the Baltic mussel Mytilus trossulus

The effect of mitochondrial recombination on fertilization success in blue mussels

The presence of doubly uniparental inheritance (DUI) in bivalves represents a unique mode of mitochondrial transmission, whereby paternal (male-transmitted M-type) and maternal (female-transmitted F-type) haplotypes are transmitted to offspring separately. Male embryos retain both haplotypes, but the M-type is selectively removed from females. Due to the presence of heteroplasmy in males, mtDNA can recombine resulting in a 'masculinized' haplotype referred to as Mf-type. While mtDNA recombination is usually rare, it has been recorded in multiple mussel species across the Northern Hemisphere. Given that mitochondria are the powerhouse of the cell, different mtDNA haplotypes may have different selective advantages under diverse environmental conditions. This may be particularly important for sperm fitness and fertilization success. In this study we aimed to i) determine the presence, prevalence of the Mf-type in Australian blue mussels (Mytilus sp.) and ii) investigate the effect of Mf-mtDNA on sperm performance (a fitness correlate). We found a high prevalence of recombined mtDNA (≈35 %) located within the control region of the mitochondrial genome, which occurred only in specimens that contained Southern Hemisphere mtDNA. The presence of two female mitotypes were identified in the studied mussels, one likely originating from the Northern Hemisphere, and the other either representing the endemic M. planulatus species or introduced genotypes from the Southern Hemisphere. Despite having recombination events present in a third of the studied population, analysis of sperm performance indicated no difference in fertilization success related to mitotype.

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis

We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.

Two lineages of bivalve transmissible neoplasia affect the blue mussel Mytilus trossulus Gould in the subarctic Sea of Okhotsk

There are increasing findings of the bivalve transmissible neoplasia derived from the Pacific mussel Mytilus trossulus (MtrBTN) in populations of different Mytilus species worldwide. The Subarctic is an area where this disease has not yet been sought despite the fact that Mytilus spp. are widespread there, and M. trossulus itself is a boreal species. We used flow cytometry of the hemolymph, hemocytology and histology to diagnose disseminated neoplasia in a sample of M. trossulus from Magadan in the subarctic Sea of Okhotsk. Neoplasia was identified in 11 of 214 mussels studied. Using mtDNA COI sequencing, we revealed genotypes identical or nearly identical to known MtrBTN ones in the hemolymph of most of the diseased mussels. Both MtrBTN evolutionary lineages have been identified, the widespread MtrBTN2, and MtrBTN1, so far only known from M. trossulus in British Columbia on the other side of the Pacific from Magadan. In addition, MtrBTN2 was represented by two common diverged mtDNA haplolineages. These conclusions were confirmed for selected cancerous mussels by molecular cloning of COI and additional nuclear and mtDNA genes. On the background of high genetic diversity, different cancers were similar in terms of ploidy (range 4.0 - 5.8n) and nuclear to cell ratio. Our study provides the first description of neoplasia and MtrBTN in mussels from the Sea of Okhotsk and from the Subarctic, of both MtrBTN1 and MtrBTN2 in the same mussel population, and the first direct comparison between these transmissible cancers.

Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria

Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.

Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)

Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.

Actively transcribed and expressed atp8 gene in Mytilus edulis mussels

Background

Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial.

Results

Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis.

Conclusion

Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).

Distribution and frequency of mitochondrial DNA polymorphisms in blue mussel (Mytilus edulis) populations of southwestern Nova Scotia (Canada)

The Atlantic blue mussel (Mytilus edulis Linnaeus, 1758) exhibits doubly uniparental inheritance of mitochondrial (mt) DNA. Females are usually homoplasmic for a female-transmitted mt genome (the F type) and males are heteroplasmic for an F type and a male-transmitted mt genome (the M type). F types can undergo “role-reversal” events, resulting in new male-transmitted mtDNA genomes known as recently masculinized (RM) types that co-occur in populations with evolutionarily older standard-male (SM) types. Phylogenetic analyses have shown that RM types periodically replace SM types. It has also been shown that sperm with RM mtDNA have greater swimming velocity and more efficient components of the electron transport chain compared to sperm with SM mtDNA, thus leading to the hypothesis that RM sperm may have a selective advantage over SM sperm. The present study examines the distribution of RM and SM mitotypes in male M. edulis (n = 225) from 13 localities in southwestern Nova Scotia (Canada). The SM type was more common in all populations, with the proportion of RM types ranging from 0% to 24.1%. The highest proportion of RM types was observed in an aquaculture operation. Analyses of additional populations are required to evaluate the selective pressures affecting the geographic distribution of RM and SM mitotypes in M. edulis.

Hermaphroditic freshwater mussel Anodonta cygnea does not have supranumerary open reading frames in the mitogenome

The complete mitogenome of Anodonta cygnea is 15,613 bp long. This compact, circular molecule contains the set of 37 genes, typical for invertebrate mitogenomes, in the same order and orientation as in maternally inherited genomes of other bivalves from the same subfamily. There are only two unassigned regions longer than 200 bp (266 bp and 274 bp) and no indication of any supranumerary open reading frames.

Complete female mitochondrial genome of Mytilus chilensis

The controversy surrounding the origin of antitropical distribution of Mytilus mussels and the taxonomic status of southern hemisphere populations remain unsolved, despite the efforts. One of the limiting factors remains the lack of the complete sequences of the representative mitochondrial genomes which would allow their proper comparison with the relatively well-represented northern hemisphere congeneric mussels. To fill this gap we sequenced the representative maternal (F) genome of a native Chilean mussel. The genome is 16,748bp long and structurally identical to the northern hemisphere M. edulis and M. galloprovincialis F genomes. However, the genetic distance from them (≈5%) is twice as high as the maximum distance between them (<2.5%). Thus, the notion that the name M. chilensis should be used for native Chilean Mytilus mussels, with the same rank as M. galloprovincialis and M. edulis is supported.

Sequence motifs associated with paternal transmission of mitochondrial DNA in the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae)

In the majority of metazoans paternal mitochondria represent evolutionary dead-ends. In many bivalves, however, this paradigm does not hold true; both maternal and paternal mitochondria are inherited. Herein, we characterize maternal and paternal mitochondrial control regions of the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). The maternal control region is 808bp long, while the paternal control region is longer at 2.3kb. We hypothesize that the size difference is due to a combination of repeated duplications within the control region of the paternal mtDNA genome, as well as an evolutionarily ancient recombination event between two sex-associated mtDNA genomes that led to the insertion of a second control region sequence in the genome that is now transmitted via males. In a comparison to other mytilid male control regions, we identified two evolutionarily Conserved Motifs, CMA and CMB, associated with paternal transmission of mitochondrial DNA. CMA is characterized by a conserved purine/pyrimidine pattern, while CMB exhibits a specific 13bp nucleotide string within a stem and loop structure. The identification of motifs CMA and CMB in M. modiolus extends our understanding of Sperm Transmission Elements (STEs) that have recently been identified as being associated with the paternal transmission of mitochondria in marine bivalves.

Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels

Recombination in the control region (CR) of Mytilus mitochondrial DNA (mtDNA) was originally reported based on the relatively short, sequenced fragments of mitochondrial genomes. Recombination outside the CR has been reported recently with the suggestion that such processes are common in Mytilus. We have fully sequenced a set of 11 different mitochondrial haplotypes representing the high diversity of paternally inherited mitochondrial genomes of Baltic Sea Mytilus mussels, including the haplotype close to the native Mytilus trossulus mitochondrial genome, which was thought to have been entirely eliminated from this population. Phylogenetic and comparative analysis showed that the recombination is limited to the vicinity of the CR in all sequenced genomes. Coding sequence comparison indicated that all paternally inherited genomes showed increased accumulation of nonsynonymous substitutions, including the genomes which switched their transmission route very recently. The acquisition of certain CR sequences through recombination with highly divergent paternally inherited genomes seems to precede and favor the switch, but it is not a prerequisite for this process. Interspecies hybridization in the Baltic Sea during the recent 10,000 years created conditions for both structural and evolutionary mitochondrial instability which resulted in the observed variation and dynamics of mtDNA in Baltic Sea Mytilus mussels. In conclusion, the data shows that the effects of mitochondrial recombination are limited to the CR of few phylogenetic lineages.

Complete male mitochondrial genomes of European Mytilus edulis mussels

Doubly uniparental inheritance (DUI) results in the existence of two gender-specific, divergent mtDNA lineages within a single species. Under DUI, the female genome (F) is transmitted from mothers to the whole offspring, and the male genome (M) is transmitted exclusively from fathers to sons. This system was first described in a marine mussels Mytilus edulis inhabiting European coastal waters, over a decade ago. Despite that, the complete sequence of the M genome from the European M. edulis mussels remained unknown. Here we announce it for the first time. The announcement is based on the two haplotypes isolated from heteroplasmic males of European M. edulis sampled at two moderately distant locations: southern North Sea and western Baltic. The two M genomes are quite similar both in length (16,631 and 16,632 bp) and in sequence (98.3%). Furthermore, both newly sequenced genomes are closely related to the genomes described from Baltic M. trossulus.

The F type mitochondrial genome of hard-shelled mussel: Mytilus coruscus (Mytiloida, Mytilidae)

We determined the complete mitochondrial genome of the female hard-shelled mussel Mytilus coruscus (Gould, 1869) (F type). The F type genome is composed of 16,642 bp in length including 12 protein coding genes (PCGs), 2 rRNA and 23 tRNA with the same gene content and order as the other Mytilus species which is characterized by the absence of the ATPase8 gene and addition of tRNA(Met) (AUA). The nucleotide composition of the genome shows that the percentage of A+T (63.2%) is higher than those of M. edulis complex species (M. edulis, M. galloprovincialis, M. trossulus) but lower than that of M. californianus. The F type mitochondrial genome of M. coruscus will provide useful information on the evolutionary history of the Mytilus species in the family Mitilidae.

Co-expressed mitochondrial genomes: recently masculinized, recombinant mitochondrial genome is co-expressed with the female-transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea

BACKGROUND

Few exceptions have been described from strict maternal inheritance of mitochondrial DNA in animals, including sea mussels (Mytilidae), clams (Donacidae, Veneridae and Solenidae) and freshwater mussels (Unionoidae) order. In these bivalves mitochondria and their DNA are transferred through two separate routes. The females inherit only the maternal mitochondrial DNA whereas the males inherit maternal as well as paternal mitochondrial DNA, which is usually present only in gonads and sperm. The mechanism controlling this phenomenon is unclear but leads to the existence of two separate mitochondrial DNA lineages in a single species. The lineages are usually well differentiated: up to 20-50% divergence in nucleotide sequence. Occasionally, a maternal mitochondrial DNA can invade the paternal transmission route, eventually replacing the diverged M-type and lowering the divergence. Such role reversal (masculinization) event has happened recently in the Mytilus population of the Baltic Sea which consists of M. edulis × M. trossulus hybrids, but the functional status of the resulting mitochondrial genome was unknown.

RESULTS

In this paper we sequenced transcripts from one specimen that was identified as male carrying both the female mitochondrial genome and a recently masculinized mitochondrial genome. Additionally, the analysis of the control region has showed that the recently masculinized, recombinant genome, not only has an M-type control region and all coding regions derived from the F-type, but also is transcriptionally active along side the maternally inherited F-type genome. In the comparative analysis, the two genomes exhibit different substitution patterns, typical for the M vs. F genome comparisons. The genetic distances and ratios of non-synonymous substitutions also suggest that one of the genomes is transitioning from the maternal to the paternal inheritance mode, consistent with its recent masculinization.

CONCLUSION

We have shown, for the first time, that the recently masculinized mitochondrial genome is active and that it accumulates excess of non-synonymous substitutions across its coding sequence. This suggests, that, under certain cytonuclear incompatibility conditions, masculinization may serve to restore the endangered functionality of the paternally inherited genome. This is also another example of a mitochondrial genome in which the recombination in the control region predated its transition from paternal to maternal transmission route.

Sliding window analyses for optimal selection of mini-barcodes, and application to 454-pyrosequencing for specimen identification from degraded DNA

DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential 'mini-barcodes' for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

BACKGROUND

Bivalves are very ancient and successful conchiferan mollusks (both in terms of species number and geographical distribution). Despite their importance in marine biota, their deep phylogenetic relationships were scarcely investigated from a molecular perspective, whereas much valuable work has been done on taxonomy, as well as phylogeny, of lower taxa.

METHODOLOGY/PRINCIPAL FINDINGS

Here we present a class-level bivalve phylogeny with a broad sample of 122 ingroup taxa, using four mitochondrial markers (MT-RNR1, MT-RNR2, MT-CO1, MT-CYB). Rigorous techniques have been exploited to set up the dataset, analyze phylogenetic signal, and infer a single final tree. In this study, we show the basal position of Opponobranchia to all Autobranchia, as well as of Palaeoheterodonta to the remaining Autobranchia, which we here propose to call Amarsipobranchia. Anomalodesmata were retrieved as monophyletic and basal to (Heterodonta + Pteriomorphia).

CONCLUSIONS/SIGNIFICANCE

Bivalve morphological characters were traced onto the phylogenetic trees obtained from the molecular analysis; our analysis suggests that eulamellibranch gills and heterodont hinge are ancestral characters for all Autobranchia. This conclusion would entail a re-evaluation of bivalve symplesiomorphies.

Evidence for a fourteenth mtDNA-encoded protein in the female-transmitted mtDNA of marine Mussels (Bivalvia: Mytilidae)

Background

A novel feature for animal mitochondrial genomes has been recently established: i.e., the presence of additional, lineage-specific, mtDNA-encoded proteins with functional significance. This feature has been observed in freshwater mussels with doubly uniparental inheritance of mtDNA (DUI). The latter unique system of mtDNA transmission, which also exists in some marine mussels and marine clams, is characterized by one mt genome inherited from the female parent (F mtDNA) and one mt genome inherited from the male parent (M mtDNA). In freshwater mussels, the novel mtDNA-encoded proteins have been shown to be mt genome-specific (i.e., one novel protein for F genomes and one novel protein for M genomes). It has been hypothesized that these novel, F- and M-specific, mtDNA-encoded proteins (and/or other F- and/or M-specific mtDNA sequences) could be responsible for the different modes of mtDNA transmission in bivalves but this remains to be demonstrated.

Methodology/Principal Findings

We investigated all complete (or nearly complete) female- and male-transmitted marine mussel mtDNAs previously sequenced for the presence of ORFs that could have functional importance in these bivalves. Our results confirm the presence of a novel F genome-specific mt ORF, of significant length (>100aa) and located in the control region, that most likely has functional significance in marine mussels. The identification of this ORF in five Mytilus species suggests that it has been maintained in the mytilid lineage (subfamily Mytilinae) for ∼13 million years. Furthermore, this ORF likely has a homologue in the F mt genome of Musculista senhousia, a DUI-containing mytilid species in the subfamily Crenellinae. We present evidence supporting the functionality of this F-specific ORF at the transcriptional, amino acid and nucleotide levels.

Conclusions/Significance

Our results offer support for the hypothesis that “novel F genome-specific mitochondrial genes” are involved in key biological functions in bivalve species with DUI.

Complete sequences of maternally inherited mitochondrial genomes in mussels Unio pictorum (Bivalvia, Unionidae)

Mitochondrial genomes are frequently used to infer phylogenetic relationships. Some taxa are, however, poorly represented. To facilitate better understanding of the potential of mitochondrial genome data in freshwater mussels, we present here, for the first time, the mitochondrial sequences of 4 complete F-type mitochondrial genomes from the European freshwater bivalve Unio pictorum (Unionidae). These genomes are very compact (15,761 bp) but have a typical gene complement for bilaterian mitochondrial genomes and a very similar organization to other unionid genomes available in databases. Very low nucleotide diversity within the species suggests a small effective population size of Polish U. pictorum, a phenomenon of potential importance for environmental management policies.

Mytilus trossulus in Northern Europe

From data on allozyme, nuclear DNA and mitochondrial DNA markers, we show that the originally North Pacific/Northwest Atlantic mussel Mytilus trossulus is widespread on North European coasts, earliM. trossuluser thought to be inhabited only by Mytilus edulis. Several local occurrences of , interspersed with a dominant M. edulis, were recorded on the North Sea, Norwegian Sea and Barents Sea coasts of Norway and the Barents and White Sea coasts of Kola Peninsula in Russia. The proportion of M. trossulus genetic background observed at any one site varied from 0 to 95%. These new occurrences are not related to the previously known, introgressed M. trossulus population that occupies the Baltic Sea. The new northern occurrences retain both the F and M M. trossulus mitochondria, which have been lost from the Baltic stock. While hybridization takes place wherever M. trossulus and M. edulis meet, the extent of hybrization varies between the different contact areas. Hybrids are rare, and the hybrid zones are bimodal in the northern areas; more interbreeding has taken place further south in Norway, but even there genotypic disequilibria are higher than those in the steep transition zone between the Baltic mussel and M. edulis: there is no evidence of a collapse toward a hybrid swarm unlike in the Baltic. The Barents and White Sea M. trossulus are genetically slightly closer to the NW Atlantic than NE Pacific populations, while the Baltic mussel has unique features distinguishing it from the others. We postulate that the presence of M. trossulus in Northern Europe is a result of repeated independent inter- or transoceanic cryptic invasions of various ages, up to recent times.

The atypical presence of the paternal mitochondrial DNA in somatic tissues of male and female individuals of the blue mussel species Mytilus galloprovincialis

BACKGROUND

In animals mtDNA inheritance is maternal except in certain molluscan bivalve species which have a paternally inherited mitochondrial genome (genome M) along with the standard maternal one (genome F). Normally, the paternal genome occurs in the male gonad, but it can be often found, as a minority, in somatic tissues of males and females. This may happen in two ways. One is through "sperm mtDNA leakage" into somatic tissues, a deviation from the normal situation in which the sperm mtDNA vanishes in females or ends up exclusively in the germ line of males. The other is through "egg heteroplasmy", when the egg contains, in small quantities, the paternal genome in addition to maternal genome.

FINDINGS

To test the two hypotheses, we compared the sequences of one of the most variable domains of the M molecule in a somatic tissue (foot) and in the sperm of ten male and in the foot of ten female individuals of M. galloprovincialis. Presence of the M genome was rarer in the foot of females than males. The M genome in the sperm and in the foot of males was identical.

CONCLUSIONS

Given that the surveyed region differs from individual to individual, the identity of the M genome in the foot and the sperm of males supports strongly the hypothesis that, at least for the tissue examined, the presence of the M genome is due to sperm mtDNA leakage.

Scottish Mytilus trossulus mussels retain ancestral mitochondrial DNA: complete sequences of male and female mtDNA genomes

Mytilus trossulus mussels occur in North America and in the Baltic Sea. Recently genetic markers for the three Mytilus subspecies M. edulis, M. galloprovincialis, and M. trossulus, have been detected at Loch Etive in Scotland suggesting mixed ancestry for this population. Of particular interest is the evidence that M. trossulus occurs at Loch Etive because it had not previously been reported in the British Isles. In the present study, analysis of subspecies-specific diagnostic nuclear DNA markers confirms the presence of a high frequency of mussels with M. trossulus ancestry at Loch Etive. The genetic structure suggests hybridisation at an intermediate stage compared with North American populations, where there is little hybridisation, and Baltic populations where there is extensive introgression. This points strongly against a Baltic origin for Loch Etive M. trossulus. The F and M mitochondrial DNA (mtDNA) genomes of Baltic M. trossulus are similar in sequence to the corresponding genomes in M. edulis and believed to be derived by introgression from that subspecies. Both F and M mtDNA genomes are observed at Loch Etive consistent with the presence of doubly uniparental inheritance. Here we provide the complete sequences of the three M. trossulus mtDNA genomes (one F and two M) from Loch Etive. These genomes are extremely similar to the corresponding genomes from ancestral M. trossulus in America but divergent from the genomes for Baltic M. trossulus. This is the first report of ancestral M. trossulus mtDNA genomes in Europe. The F and M genomes are diverged by 26% in nucleotide sequence, similar to other Mytilus F and M genomes. The gene arrangement in the sequenced genomes is also similar to that in other sequenced Mytilus mtDNA genomes. However the two sequenced M genomes differ by 960bp which is caused by a duplication in the main noncoding region (CR). This duplication has not so far been observed in North American populations of M. trossulus. The coding regions of the Loch Etive genomes have no features suggesting that they are other than functional genomes and have K(a)/K(s) values in coding regions less than one indicative of purifying selection. Estimates of divergence times were made for both genomes and are consistent with invasion of Loch Etive by M. trossulus towards the end of the last glacial period.

Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA

Background

Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata).

Results

Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida).

Conclusion

The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.

Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia: Mytilidae): identification of the "missing" ATPase 8 gene

Bivalve species are characterized by extraordinary variability in terms of mitochondrial (mt) genome size, gene arrangement and tRNA gene number. Many species are thought to lack the mitochondrial protein-coding gene atp8. Of these species, the Mytilidae appears to be the only known taxon with doubly uniparental inheritance of mtDNA that does not possess the atp8 gene. This raises the question as to whether mytilids have completely lost the ATP8 protein, whether the gene has been transferred to the nucleus or whether they possess a highly modified version of the gene/protein that has led to its lack of annotation. In the present study, we re-investigated all complete (or nearly complete) F and M mytilid mt genomes previously sequenced for the presence of conserved open reading frames (ORFs) that might code for ATP8 and/or have other functional importance in these bivalves. We also revised the annotations of all available complete mitochondrial genomes of bivalves and nematodes that are thought to lack atp8 in an attempt to detect it. Our results indicate that a novel mytilid ORF of significant length (i.e., the ORF is >85 amino acids in length), with complete start and stop codons, is a candidate for the atp8 gene: (1) it possesses a pattern of evolution expected for a protein-coding gene evolving under purifying selection (i.e., the 3rd>1st>2nd codon pattern of evolution), (2) it is actively transcribed in Mytilus species, (3) it has one predicted transmembrane helix (as do other metazoan ATP8 proteins), (4) it has conserved functional motifs and (5), comparisons of its amino acid sequence with ATP8 sequences of other molluscan or bivalve species reveal similar hydropathy profiles. Furthermore, our revised annotations also confirmed the mt presence of atp8 in almost all bivalve species and in one nematode species. Our results thus support recognizing the presence of ATPase 8 in most bivalves mt genomes (if not all) rather than the continued characterization of these genomes as lacking this gene.

Comparative mitochondrial genomics of freshwater mussels (Bivalvia: Unionoida) with doubly uniparental inheritance of mtDNA: gender-specific open reading frames and putative origins of replication

Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of gender-associated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general. Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one F-specific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (O(H)) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (O(L)) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or gender-specific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

The mitochondrial genome (mtDNA) of Metazoa is a good model system for evolutionary genomic studies and the availability of more than 1000 sequences provides an almost unique opportunity to decode the mechanisms of genome evolution over a large phylogenetic range. In this paper, we review several structural features of the metazoan mtDNA, such as gene content, genome size, genome architecture and the new parameter of gene strand asymmetry in a phylogenetic framework. The data reviewed here show that: (1) the plasticity of Metazoa mtDNA is higher than previously thought and mainly due to variation in number and location of tRNA genes; (2) an exceptional trend towards stabilization of genomic features occurred in deuterostomes and was exacerbated in vertebrates, where gene content, genome architecture and gene strand asymmetry are almost invariant. Only tunicates exhibit a very high degree of genome variability comparable to that found outside deuterostomes. In order to analyse the genomic evolutionary process at short evolutionary distances, we have also compared mtDNAs of species belonging to the same genus: the variability observed in congeneric species significantly recapitulates the evolutionary dynamics observed at higher taxonomic ranks, especially for taxa showing high levels of genome plasticity and/or fast nucleotide substitution rates. Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups.