Evidence that the large noncoding sequence is the main control region of maternally and paternally transmitted mitochondrial genomes of the marine mussel (Mytilus spp.)

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.

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance

In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.

A Systematic Review of the Impact of Mitochondrial Variations on Male Infertility

According to current estimates, infertility affects one in four couples trying to conceive. Primary or secondary infertility can be due either to both partners or only to the man or the woman. Up to 15% of infertility cases in men can be attributed to genetic factors that can lead to irreversible partial or complete spermatogenic arrest. The increased use of assisted reproductive technology (ART) has provided not only insights into the causes of male infertility but also afforded a diagnostic tool to detect and manage this condition among couples. Genes control a variety of physiological attributes, such as the hypothalamic–pituitary–gonadal axis, development, and germ cell differentiation. In the era of ART, it is important to understand the genetic basis of infertility so as to provide the most tailored therapy and counseling to couples. Genetic factors involved in male infertility can be chromosome abnormalities or single-gene disorders, mitochondrial DNA (mtDNA) mutations, Y-chromosome deletions, multifactorial disorders, imprinting disorders, or endocrine disorders of genetic origin. In this review, we discuss the role of mitochondria and the mitochondrial genome as an indicator of sperm quality and fertility.

Mitogenome sequence comparison in the endangered congeneric Pinna nobilis and Pinna rudis bivalves

BACKGROUND

The pen shells Pinna nobilis and Pinna rudis are large wedge-shaped bivalve molluscs. Both species are threatened by different anthropogenic pressures. In the last few years, P. nobilis populations have significantly reduced due to massive mortality events. The complete mitochondrial DNA sequences of these congeneric species have been determined and compared for the first time.

RESULTS

The mitogenome sequences of P. nobilis and P. rudis were 18,919 bp and 18,264 bp in length, respectively. Each mitogenome is composed of 12 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA (tRNAs) genes and non-coding regions. A putative Adenosine Triphosphate synthase subunit 8 gene could only be proposed for P. nobilis. Both newly sequenced mitogenomes present a conserved gene order between them, comparable to the closely related Atrina pectinata, but global arrangement greatly differs from other available bivalve mitochondrial sequences. Multiple copies of tRNA-Cys were identified, located in different positions probably due to mechanisms of mitochondrial genome rearrangements, and detected 2 and 3 times in P. rudis and in P. nobilis, respectively.

CONCLUSION

A close relationship was shown between Pinna species and Atrina pectinata and a consistent clustering showing a monophyletic origin of Pinnidae family sequences was evidenced. The mitochondrial genomes will provide a valuable genetic resource for further studies on population genetics and species identification.

Expanding the Search for Sperm Transmission Elements in the Mitochondrial Genomes of Bivalve Mollusks

Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as the sperm transmission element (STE), helps protect male-transmitted mitochondria from destruction during spermatogenesis. Subsequent studies found similar, yet divergent, STE motifs in other marine mussels. Here, we extend the in silico search for mtDNA signatures resembling known STEs. This search is carried out for the large unassigned regions of 157 complete mitochondrial genomes from within the Mytiloida, Veneroida, Unionoida, and Ostreoida bivalve orders. Based on a sliding window approach, we present evidence that there are additional putative STE signatures in the large unassigned regions of several marine clams and freshwater mussels with DUI. We discuss the implications of this finding for interpreting the origin of doubly uniparental inheritance in ancestral bivalve mollusks, as well as potential future in vitro and in silico studies that could further refine our understanding of the early evolution of this unusual system of mtDNA inheritance.

Gender-Associated Mitochondrial DNA Heteroplasmy in Somatic Tissues of the Endangered Freshwater Mussel Unio crassus (Bivalvia: Unionidae): Implications for Sex Identification and Phylogeographical Studies

Some bivalve species possess two independent mitochondrial DNA lineages: maternally (F-type) and paternally (M-type) inherited. This phenomenon is called doubly uniparental inheritance. It is generally agreed that F-type mtDNA is typically present in female somatic and gonadal tissues as well as in male somatic tissues, whereas the M-type mtDNA occurs only in male germ line and gonadal tissue. In the present study, the mtDNA heteroplasmy (for both F and M genomes) in male somatic tissues of Unio crassus (Philipsson, 1788), species threatened with extinction, has been confirmed. Taking advantage from the presence of Mcox1 marker only in male somatic tissues, we developed a new method of sex identification in this endangered species, using nondestructive tissue sampling. Probability of correct sex identification was estimated at 97.5%. The present study is the first report on gender-associated mitochondrial DNA heteroplasmy in male somatic tissues of thick-shelled river mussel and first approach to U. crassus sex identification at molecular level. Our study also confirmed the utility of paternally inherited Mcox1 gene fragment as a complementary molecular tool for resolving phylogeographical relationships among populations of thick-shelled river mussel.

The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)

Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point.

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 southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex

Marine blue mussels (Mytilus spp.) are widespread species that exhibit an antitropical distribution with five species occurring in the Northern Hemisphere (M. trossulus, M. edulis, M. galloprovincialis, M. californianus and M. coruscus) and three in the Southern Hemisphere (M. galloprovincialis, M. chilensis and M. platensis). Species limits in this group remain controversial, in particular for those forms that live in South America. Here we investigated structural characteristics of marine mussels mitogenomes, based on published F mtDNA sequences of Northern Hemisphere species and two newly sequenced South American genomes, one from the Atlantic M. platensis and another from the Pacific M. chilensis. These mitogenomes exhibited similar architecture to those of other genomes of Mytilus, including the presence of the Atp8 gene, which is missing in most of the other bivalves. Our evolutionary analysis of mitochondrial genes indicates that purifying selection is the predominant force shaping the evolution of the coding genes. Results of our phylogenetic analyses supported the monophyly of Pteriomorphia and fully resolved the phylogenetic relationships among its five orders. Finally, the low genetic divergence of specimens assigned to M. chilensis and M. platensis suggests that these South American marine mussels represent conspecific variants rather than distinct species.

The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii

Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of Meretrix lamarckii, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in M. lamarckii M-cox2 gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of M. lamarckii. Even if no direct involvement in DUI process has been demonstrated so far, the finding of cox2 insertions and supernumerary ORFs in M. lamarckii both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.

A First Insight into the Genome of the Filter-Feeder Mussel Mytilus galloprovincialis

Mussels belong to the phylum Mollusca, one of the largest and most diverse taxa in the animal kingdom. Despite their importance in aquaculture and in biology in general, genomic resources from mussels are still scarce. To broaden and increase the genomic knowledge in this family, we carried out a whole-genome sequencing study of the cosmopolitan Mediterranean mussel (Mytilus galloprovincialis). We sequenced its genome (32X depth of coverage) on the Illumina platform using three pair-end libraries with different insert sizes. The large number of contigs obtained pointed out a highly complex genome of 1.6 Gb where repeated elements seem to be widespread (~30% of the genome), a feature that is also shared with other marine molluscs. Notwithstanding the limitations of our genome sequencing, we were able to reconstruct two mitochondrial genomes and predict 10,891 putative genes. A comparative analysis with other molluscs revealed a gene enrichment of gene ontology categories related to multixenobiotic resistance, glutamate biosynthetic process, and the maintenance of ciliary structures.

A protein binding site in the M mitochondrial genome of Mytilus galloprovincialis may be responsible for its paternal transmission

Sea mussels (genus Mytilus) have two mitochondrial genomes in obligatory co-existence, one that is transmitted through the egg and the other through the sperm. The phenomenon, known as Doubly Uniparental Inheritance (DUI) of mitochondrial DNA (mtDNA), is presently known to occur in more than 40 molluscan bivalve species. Females and the somatic tissues of males contain mainly the maternal (F) genome. In contrast, the sperm contains only the paternal (M) genome. Through electrophoretic mobility shift assay (EMSA) experiments we have identified a sequence element in the control region (CR) of the M genome that acts as a binding site for the formation of a complex with a protein factor that occurs in the male gonad. An adenine tract upstream to the element is also essential for the formation of the complex. The reaction is highly specific. It does not occur with protein extracts from the female gonad or from a male or female somatic tissue. Further experiments showed that the interaction takes place in mitochondria surrounding the nucleus of the cells of male gonads, suggesting a distinct role of perinuclear mitochondria. We propose that at a certain point during spermatogenesis mitochondria are subject to degradation and that perinuclear mitochondria with the M mtDNA-protein complex are protected from this degradation with the result that mature spermatozoa contain only the paternal mitochondrial genome.

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.

Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages

Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.

Mitochondrial control region variability in Mytilus galloprovincialis populations from the central-Eastern Mediterranean Sea

The variable domain 1 (VD1) domain of the control region and a small segment of the rrnaL gene of the F mtDNA type were sequenced and analyzed in 174 specimens of Mytilus galloprovincialis. Samples were collected from eight locations in four Central-Eastern (CE) Mediterranean countries (Italy, Croatia, Greece and Turkey). A new primer, specific for the F mtDNA type, was designed for the sequencing procedure. In total 40 different haplotypes were recorded, 24 of which were unique. Aside from the two populations situated in Thermaikos gulf (Northern Aegean, Greece), relatively high levels of haplotype and nucleotide diversity were estimated for both Central and Eastern Mediterranean populations. Eight out of the 40 haplotypes were shared by at least three populations while two of them were found in all populations. ΦST and cluster analysis revealed lack of structuring among CE Mediterranean populations with the exception of those located at the Sea of Marmara and Croatian coast which were highly differentiated. Apart from the species' inherit dispersal ability, anthropogenic activities, such as the repeated translocations of mussel spat, seem to have played an important role in shaping the current genetic population structure of CE M. galloprovincialis mussels.

Recombinant mitochondrial genome with standard transmission route from Mediterranean mussel Mytilus galloprovincialis

Several bivalve species, including marine mussels Mytilus are atypical in having two gender-specific and highly divergent mtDNA genomes. This peculiar genetic system allows not only the recombination to occur but also facilitates its detection. Previous reports associated the existence of mosaic recombinant haplotypes with the switch of their transmission route. Here we report nearly complete sequence of a mitochondrial genome isolated from a homoplasmic female individual of Mediterranean Mytilus galloprovincialis. The genome has clear phylogenetic affinity with and organization identical to the M. galloprovincialis female haplotypes, in the coding part. However, the genome is very large, approximately 20,600 bp long, exclusively due to a long and complex control region. It contains an array of repeats, some of which are degenerated. A large part of the control region is derived from the paternal genome. This finding shows that not all haplotypes with recombinant control regions must be paternally inherited in Mytilus.

The rRNA and tRNA transcripts of maternally and paternally inherited mitochondrial DNAs of Mytilus galloprovincialis suggest presence of a "degradosome" in mussel mitochondria and necessitate the re-annotation of the l-rRNA/CR boundary

Species of the genus Mytilus carry two mitochondrial genomes in obligatory coexistence; one transmitted though the eggs (the F type) and one through the sperm (the M type). We have studied the 3' and 5' ends of rRNA and tRNA transcripts using RT-PCR and RNA circularization techniques in both the F and M genomes of Mytilus galloprovincialis. We have found polyadenylated and non-adenylated transcripts for both ribosomal and transfer RNAs. In all these genes the 5' ends of the transcripts coincided with the first nucleotide of the annotated genes, but the 3' ends were heterogeneous. The l-rRNA 3' end is 47 or 48 nucleotides upstream from the one assigned by a previous annotation, which makes the adjacent first domain (variable domain one, VD1) of the main control region (CR) correspondingly longer. We have observed s-rRNA and l-rRNA transcripts with truncated 3' end and polyadenylated tRNA transcripts carrying the CCA trinucleotide. We have also detected polyadenylated RNA remnants carrying the sequences of the control region, which strongly suggests RNA degradation activity and thus presence of degradosomes in Mytilus mitochondria.

The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae)

Musculista senhousia is a marine mussel with doubly uniparental inheritance (DUI) of mitochondria. In this study we analyzed the largest unassigned region (LUR) of its female- and male-transmitted mitochondrial genomes, described their fine characteristics and searched for shared features. Our results suggest that both LURs contain the control region of their respective mitochondrial genomes. The female-transmitted control region is duplicated in tandem, with the two copies evolving in concert. This makes the F-mtDNA of M. senhousia the first Bivalve mitochondrial genome with this feature. We also compared M. senhousia control regions to that of other Mytilidae, and demonstrated that signals for basic mtDNA functions are retained over evolutionary times even among the fast-evolving mitochondrial genomes of DUI species. Finally, we discussed how similarities between female and male LURs may be explained in the context of DUI evolution and if the duplicated female control region might have influenced the DUI system in this species.

Mitochondrial DNA transcription levels during spermatogenesis and early development in doubly uniparental inheritance of the mitochondrial DNA system of the blue mussel Mytilus galloprovincialis

In some species of bivalve, there are two highly diverged mitochondrial genomes, one found in all individuals (F type) and the other normally in males only (M type). In Mytilus, a maternally-dependent sex ratio of the progeny has been reported. Some females almost exclusively produce daughters, while others produce a high proportion of sons. We previously reported that in M. galloprovincialis, M type mtDNA copy number may be maintained during spermatogenesis and the development of larvae of male-biased mothers to sustain the doubly uniparental inheritance system. In this study, we investigated transcription levels of M type mtDNA before and after fertilization to understand its function in the germ line. First, we quantified transcription levels of M type mtDNA in testicular cells dissected using laser-capture micro-dissection. The transcription levels of M type mtDNA were not significantly different between spermatogonia and spermatocytes versus spermatids and spermatozoa. Next, we examined differences in transcription levels of M type mtDNA between larvae from male-biased and female-biased mothers. The transcription levels of M type mtDNA significantly increased 24 and 48 h after fertilization in male-biased crosses. By contrast, transcription levels significantly decreased in female-biased crosses. These results suggest M type mtDNA may play a role in early germ line formation.

Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system

Despite its functional conservation, the mitochondrial genome (mtDNA) presents strikingly different features among eukaryotes, such as size, rearrangements, and amount of intergenic regions. Nonadaptive processes such as random genetic drift and mutation rate play a fundamental role in shaping mtDNA: the mitochondrial bottleneck and the number of germ line replications are critical factors, and different patterns of germ line differentiation could be responsible for the mtDNA diversity observed in eukaryotes. Among metazoan, bivalve mollusc mtDNAs show unusual features, like hypervariable gene arrangements, high mutation rates, large amount of intergenic regions, and, in some species, an unique inheritance system, the doubly uniparental inheritance (DUI). The DUI system offers the possibility to study the evolutionary dynamics of mtDNAs that, despite being in the same organism, experience different genetic drift and selective pressures. We used the DUI species Ruditapes philippinarum to study intergenic mtDNA functions, mitochondrial transcription, and polymorphism in gonads. We observed: 1) the presence of conserved functional elements and novel open reading frames (ORFs) that could explain the evolutionary persistence of intergenic regions and may be involved in DUI-specific features; 2) that mtDNA transcription is lineage-specific and independent from the nuclear background; and 3) that male-transmitted and female-transmitted mtDNAs have a similar amount of polymorphism but of different kinds, due to different population size and selection efficiency. Our results are consistent with the hypotheses that mtDNA evolution is strongly dependent on the dynamics of germ line formation, and that the establishment of a male-transmitted mtDNA lineage can increase male fitness through selection on sperm function.

The mitochondrial genome of the venomous cone snail Conus consors

Cone snails are venomous predatory marine neogastropods that belong to the species-rich superfamily of the Conoidea. So far, the mitochondrial genomes of two cone snail species (Conus textile and Conus borgesi) have been described, and these feed on snails and worms, respectively. Here, we report the mitochondrial genome sequence of the fish-hunting cone snail Conus consors and describe a novel putative control region (CR) which seems to be absent in the mitochondrial DNA (mtDNA) of other cone snail species. This possible CR spans about 700 base pairs (bp) and is located between the genes encoding the transfer RNA for phenylalanine (tRNA-Phe, trnF) and cytochrome c oxidase subunit III (cox3). The novel putative CR contains several sequence motifs that suggest a role in mitochondrial replication and transcription.

A unique tRNA gene family and a novel, highly expressed ORF in the mitochondrial genome of the silver-lip pearl oyster, Pinctada maxima (Bivalvia: Pteriidae)

Characteristics of mitochondrial (mt) DNA such as gene content and arrangement, as well as mt tRNA secondary structure, are frequently used in comparative genomic analyses because they provide valuable phylogenetic information. However, most analyses do not characterize the relationship of tRNA genes from the same mt genome and, in some cases, analyses overlook possible novel open reading frames (ORFs) when the 13 expected protein-coding genes are already annotated. In this study, we describe the sequence and characterization of the complete mt genome of the silver-lip pearl oyster, Pinctada maxima. The 16,994-bp mt genome contains the same 13 protein-coding genes (PCGs) and two ribosomal RNA genes typical of metazoans. The gene arrangement, however, is completely distinct from that of all other available bivalve mt genomes, and a unique tRNA gene family is observed in this genome. The unique tRNA gene family includes two trnS(-AGY) and trnQ genes, a trnM isomerism, but it lacks trnS(-CUN). We also report the first clear evidence of alloacceptor tRNA gene recruitment (trnP→trnS(-AGY)) in mollusks. In addition, a novel ORF (orfUR1) expressed at high levels is present in the mt genome of this pearl oyster. This gene contains a conserved domain, "Oxidored_q1_N", which is a member of Complex I and thus may play an important role in key biological functions. Because orfUR1 has a very similar nucleotide composition and codon bias to that of other genes in this genome, we hypothesize that this gene may have been moved to the mt genome via gene transfer from the nuclear genome at an early stage of speciation of P. maxima, or it may have evolved as a result of gene duplication, followed by rapid sequence divergence. Lastly, a 319-bp region was identified as the possible control region (CR) even though it does not correspond to the longest non-coding region in the genome. Unlike other studies of mt genomes, this study compares the evolutionary patterns of all available bivalve mt tRNA and atp8 genes.

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.

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.

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.

Paternal mtDNA and maleness are co-inherited but not causally linked in mytilid mussels

BACKGROUND

In marine mussels of the genus Mytilus there are two mitochondrial genomes. One is transmitted through the female parent, which is the normal transmission route in animals, and the other is transmitted through the male parent which is an unusual phenomenon. In males the germ cell line is dominated by the paternal mitochondrial genome and the somatic cell line by the maternal. Research to date has not allowed a clear answer to the question of whether inheritance of the paternal genome is causally related to maleness.

METHODOLOGY/PRINCIPAL FINDINGS

Here we present results from hybrid crosses, from triploid mussels and from observations of sperm mitochondria in fertilized eggs which clearly show that maleness and presence of the paternal mitochondrial genome can be decoupled. These same results show that the female mussel has exclusive control of whether her progeny will inherit the mitochondrial genome of the male parent.

CONCLUSIONS/SIGNIFICANCE

These findings are important in our efforts to understand the mechanistic basis of this unusual mode of mitochondrial DNA inheritance that is common among bivalves.

MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences

BACKGROUND

Although bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.

RESULTS

We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database http://mussel.cribi.unipd.it.

CONCLUSION

We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.

The control region of maternally and paternally inherited mitochondrial genomes of three species of the sea mussel genus Mytilus

Species of the mussel genus Mytilus possess maternally and paternally transmitted mitochondrial genomes. In the interbreeding taxa Mytilus edulis and M. galloprovincialis, several genomes of both types have been fully sequenced. The genome consists of the coding part (which, in addition to protein and RNA genes, contains several small noncoding sequences) and the main control region (CR), which in turn consists of three distinct parts: the first variable (VD1), the conserved (CD), and the second variable (VD2) domain. The maternal and paternal genomes are very similar in gene content and organization, even though they differ by >20% in primary sequence. They differ even more at VD1 and VD2, yet they are remarkably similar at CD. The complete sequence of a genome from the closely related species M. trossulus was previously reported and found to consist of a maternal-like coding part and a paternal-like and a maternal-like CR. From this and from the fact that it was extracted from a male individual, it was inferred that this is a genome that switched from maternal to paternal transmission. Here we provide clear evidence that this genome is the maternal genome of M. trossulus. We have found that in this genome the tRNA(Gln) in the coding region is apparently defective and that an intact copy of this tRNA occurs in the CR, that one of the two conserved domains is missing essential motifs, and that one of the two first variable domains has a high rate of divergence. These features may explain the large size and mosaic structure of the CR of the maternal genome of M. trossulus. We have also obtained CR sequences of the maternal and paternal genomes of M. californianus, a more distantly related species. We compare the control regions from all three species, focusing on the divergence among genomes of different species origin and among genomes of different transmission routes.

Pleistocene separation of mitochondrial lineages of Mytilus spp. mussels from Northern and Southern Hemispheres and strong genetic differentiation among southern populations

Smooth-shelled mussels, Mytilus spp., have an antitropical distribution. In the Northern Hemisphere, the M. edulis complex of species is composed of three genetically well delineated taxa: M. edulis, M. galloprovincialis and M. trossulus. In the Southern Hemisphere, morphological characters, allozymes and intron length polymorphisms suggest that Mytilus spp. populations from South America and Kerguelen Islands are related to M. edulis and those from Australasia to M. galloprovincialis. On the other hand, a phylogeny of the 16S rDNA mitochondrial locus demonstrates a clear distinctiveness of southern mussels and suggests that they are related to Mediterranean M. galloprovincialis. Here, we analysed the faster-evolving cytochrome oxidase subunit I locus. The divergence between haplotypes of populations from the two hemispheres was confirmed and was found to predate the divergence between haplotypes of northern M. edulis and M. galloprovincialis. In addition, strong genetic structure was detected among the southern samples, revealing three genetic entities that correspond to (1) South America and Kerguelen Island, (2) Tasmania, (3) New Zealand. Using the trans-Arctic interchange as a molecular clock calibration, we estimated the time since divergence of populations from the two hemispheres to be between 0.5 million years (MY) and 1.3 MY (average 0.84 MY). The contrasting patterns observed for the nuclear and the organelle genomes suggested two alternative, complex scenarios: two trans-equatorial migrations and the existence of differential barriers to mitochondrial and nuclear gene flow, or a single trans-equatorial migration and a view of the composition of the nuclear genome biased by taxonomic preconception.

Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis

The monogonont rotifer Brachionus plicatilis is an emerging model system for a diverse array of questions in limnological ecosystem dynamics, the evolution of sexual recombination, cryptic speciation, and the phylogeny of basal metazoans. We sequenced the complete mitochondrial genome of B. plicatilis sensu strictu NH1L and found that it is composed of 2 circular chromosomes, designated mtDNA-I (11,153 bp) and mtDNA-II (12,672 bp). Hybridization to DNA isolated from mitochondria demonstrated that mtDNA-I is present at 4 times the copy number of mtDNA-II. The only nucleotide similarity between the 2 chromosomes is a 4.9-kbp region of 99.5% identity including a transfer RNA (tRNA) gene and an extensive noncoding region that contains putative D-loop and control sequence. The mtDNA-I chromosome encodes 4 proteins (ATP6, COB, NAD1, and NAD2), 13 tRNAs, and the large and small subunit ribosomal RNAs; mtDNA-II encodes 8 proteins (COX1-3, NAD3-6, and NAD4L) and 9 tRNAs. Gene order is not conserved between B. plicatilis and its closest relative with a sequenced mitochondrial genome, the acanthocephalan Leptorhynchoides thecatus, or other sequenced mitochondrial genomes. Polymerase chain reaction assays and Southern hybridization to DNA from 18 strains of Brachionus suggest that the 2-chromosome structure has been stable for millions of years. The novel organization of the B. plicatilis mitochondrial genome into 2 nearly equal chromosomes of 4-fold different copy number may provide insight into the evolution of metazoan mitochondria and the phylogenetics of rotifers and other basal animal phyla.

A mitochondrial genome with a reversed transmission route in the Mediterranean mussel Mytilus galloprovincialis

Species of the marine mussel genus Mytilus are known to contain two mitochondrial genomes, one transmitted maternally (the F genome) and the other paternally (the M genome). The two genomes have diverged by more than 20% in DNA sequence. Here we present the complete sequence of a third genome, genome C, which we found in the sperm of a Mytilus galloprovincialis male. The coding part of the new genome resembles in sequence the F genome, from which it differs by about 2% on average, but differs from the M genome by as much as the F from the M. Its major control region (CR) is more than three times larger than that of the F or the M genome and consists of repeated sequence domains of the CR of the M genome flanked by domains of the CR of the F genome. We present a sequence of events that reconstruct most parsimoniously the derivation of the C genome from the F and M genomes. The sequence consists of a duplication of CR elements of the M genome and subsequent insertion of these tandemly repeated elements in the F genome by recombination. The fact that the C genome was found as the only mitochondrial genome in the sperm of the male from which it was extracted suggests that it is transmitted paternally.

Sperm motility in Mytilus edulis in relation to mitochondrial DNA polymorphisms: implications for the evolution of doubly uniparental inheritance in bivalves

Bivalves of the families Mytilidae, Unionidae, and Veneridae have an unusual mode of mitochondrial DNA (mtDNA) transmission called doubly uniparental inheritance (DUI). A characteristic feature of DUI is the presence of two gender-associated mtDNA genomes that are transmitted through males (M-type mtDNA) and females (F-type mtDNA), respectively. Female mussels are predominantly homoplasmic with only the F-type expressed in both somatic and gonadal tissue; males are heteroplasmic with the M-type expressed in the gonad and F-type in somatic tissue for the most part. An unusual evolutionary feature of this system is that an mt genome with F-coding sequences occasionally invades the male route of inheritance (i.e., a "role reversal" event), and is thereafter transmitted as a new M-type. Phylogenetic studies have demonstrated that the new or "recently masculinized" M-types may eventually replace the older or "standard" M-types over time. To investigate whether this replacement process could be due to an advantage in sperm swimming behavior, we measured differences in motility parameters and found that sperm with the recently masculinized M-type had significantly faster curvilinear velocity and average path velocity when compared to sperm with standard M-type. This increase in sperm swimming speed could explain the multiple evolutionary replacements of standard M-types by masculinized M-types that have been hypothesized for the mytilid lineage. However, our observations do not support the hypothesis that DUI originated because it permits the evolution of mitochondrial adaptations specific to sperm performance, otherwise, the evolutionarily older, standard M genome should perform better.