Genetic parallelism between European flat oyster populations at the edge of their natural range

Although all marine ecosystems have experienced global-scale losses, oyster reefs have shown the greatest. Therefore, substantial efforts have been dedicated to restoration of such ecosystems during the last two decades. In Europe, several pilot projects for the restoration of the native European flat oyster, Ostrea edulis, recently begun and recommendations to preserve genetic diversity and to conduct monitoring protocols have been made. In particular, an initial step is to test for genetic differentiation against homogeneity among the oyster populations potentially involved in such programs. Therefore, we conducted a new sampling of wild populations at the European scale and a new genetic analysis with 203 markers to (1) confirm and study in more detail the pattern of genetic differentiation between Atlantic and Mediterranean populations, (2) identify potential translocations that could be due to aquaculture practices and (3) investigate the populations at the fringe of the geographical range, since they seemed related despite their geographic distance. Such information should be useful to enlighten the choice of the animals to be translocated or reproduced in hatcheries for further restocking. After the confirmation of the general geographical pattern of genetic structure and the identification of one potential case of aquaculture transfer at a large scale, we were able to detect genomic islands of differentiation mainly in the form of two groups of linked markers, which could indicate the presence of polymorphic chromosomal rearrangements. Furthermore, we observed a tendency for these two islands and the most differentiated loci to show a parallel pattern of differentiation, grouping the North Sea populations with the Eastern Mediterranean and Black Sea populations, against geography. We discussed the hypothesis that this genetic parallelism could be the sign of a shared evolutionary history of the two groups of populations despite them being at the border of the distribution nowadays.

Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels

The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.

Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and Crassostrea angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and the high degree of morphologic similarity. In particular, whether the presence of ecological and/or intrinsic isolating mechanisms contributes to species divergence is unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation is maintained under new environmental and demographic conditions. We generated a pseudochromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

Contribution of in Vivo Experimental Challenges to Understanding Flat Oyster Ostrea edulis Resistance to Bonamia ostreae

Bonamiosis due to the parasite Bonamia ostreae has been associated with massive mortality outbreaks in European flat oyster stocks in Europe. As eradication and treatment are not possible, the control of the disease mainly relies on transfer restriction. Moreover, selection has been applied to produce resistant flat oyster families, which present better survival and lower prevalence than non-selected oysters. In order to better understand the mechanisms involved in resistance to bonamiosis, cellular and molecular responses of 2 oyster groups (selected oysters and wild-type oysters) were analyzed in the context of experimental injection and cohabitation infections. Cellular responses including non-specific esterases detection, ROS production and phagocytosis activity were analyzed by flow cytometry. Four genes homologous to those shown to be involved in immunity were selected (Inhibitor of apotosis OeIAP, Fas ligand OeFas-ligand, Oe-SOD, and OeEc-SOD) and monitored by quantitative reverse-transcription PCR (qRT-PCR). Infected oysters showed higher phagocytosis activity than controls. Infected selected oyster show a lower phagocytosis activity which might be a protection against the parasite infection. The expression of OeIAP and OeFas-ligand gene was significantly increased in selected oysters at 5 days post-injection. OeIAP gene expression appeared to be significantly increased in wild-type oysters at 8 days post-injection. Our results suggest that resistance to bonamiosis partly relies on the ability of the oysters to modulate apoptosis.

Rapid expansion of the invasive oyster Crassostrea gigas at its northern distribution limit in Europe: Naturally dispersed or introduced?

The Pacific oyster, Crassostrea gigas, was introduced to Europe for aquaculture purposes, and has had a rapid and unforeseen northward expansion in northern Europe. The recent dramatic increase in number of C. gigas populations along the species’ northern distribution limit has questioned the efficiency of Skagerrak as a dispersal barrier for transport and survival of larvae. We investigated the genetic connectivity and possible spreading patterns between Pacific oyster populations on the southern Norwegian coast (4 localities) and Swedish and Danish populations by means of DNA microsatellite analysis of adult oysters, and by simulating larvae drift. In the simulations we used a 3D oceanographic model to explore the influence of recent climate change (1990–2010) on development, survival, and successful spreading of Danish and Swedish Pacific oyster larvae to Norwegian coastal waters. The simulations indicated adequate temperature conditions for development, survival, and settlement of larvae across the Skagerrak in warm years since 2000. However, microsatellite genotyping revealed genetic differences between the Norwegian populations, and between the Norwegian populations and the Swedish and Danish populations, the latter two populations being more similar. This patchwork pattern of genetic dissimilarity among the Norwegian populations points towards multiple local introduction routes rather than the commonly assumed unidirectional entry of larvae drifted from Denmark and Sweden. Alternative origins of introduction and implications for management, such as forecasting and possible mitigation actions, are discussed.

Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas

Background

Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe.

Methods

To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60).

Results

A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several transcripts differentially expressed between the Danish and French progenies, for which additive genetic basis is suspected (showing intermediate expression levels in hybrids, and therefore additivity). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism, known to be implicated in coordinated control and success of reproduction.

Conclusions

Observed differences suggest that adaptation of invasive populations might have occurred during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, gamete quality and fertility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1972-8) contains supplementary material, which is available to authorized users.

Genotyping of a microsatellite locus to differentiate clinical Ostreid herpesvirus 1 specimens

Ostreid herpesvirus 1 (OsHV-1) is a DNA virus belonging to the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 has been associated with mortality outbreaks in different bivalve species including the Pacific cupped oyster, Crassostrea gigas. Since 2008, massive mortality events have been reported among C. gigas in Europe in relation to the detection of a variant of OsHV-1, called μVar. Since 2009, this variant has been mainly detected in France. These results raise questions about the emergence and the virulence of this variant. The search for association between specific virus genetic markers and clinical symptoms is of great interest and the characterization of the genetic variability of OsHV-1 specimens is an area of growing interest. Determination of nucleotide sequences of PCR-amplified virus DNA fragments has already been used to characterize OsHV-1 specimens and virus variants have thus been described. However, the virus DNA sequencing approach is time-consuming in the high-scale format. Identification and genotyping of highly polymorphic microsatellite loci appear as a suitable approach. The main objective of the present study was the development of a genotyping method in order to characterise clinical OsHV-1 specimens by targeting a particular microsatellite locus located in the ORF4 area. Genotyping results were compared to sequences already available. An excellent correlation was found between the detected genotypes and the corresponding sequences showing that the genotyping approach allowed an accuraté discrimination between virus specimens.

PCR survey of 50 introns in animals: cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla

Exon Primed Intron Crossing (EPIC) markers provide molecular tools that are susceptible to be variable within species while remaining amplifiable by PCR using potentially universal primers. In this study we tested the possibility of obtaining PCR products from 50 EPIC markers on 23 species belonging to seven different phyla (Porifera, Cnidaria, Arthropoda, Nematoda, Mollusca, Annelida, Echinodermata) using 70 new primer pairs. A previous study had identified and tested those loci in a dozen species, including another phylum, Urochordata (Chenuil et al., 2010). Results were contrasted among species. The best results were achieved with the oyster (Mollusca) where 28 loci provided amplicons susceptible to contain an intron according to their size. This was however not the case with the other mollusk Crepidula fornicata, which seems to have undergone a reduction in intron number or intron size. In the Porifera, 13 loci appeared susceptible to contain an intron, a surprisingly high number for this phylum considering its phylogenetic distance with genomic data used to design the primers. For two cnidarian species, numerous loci (24) were obtained. Ecdysozoan phyla (arthropods and nematodes) proved less successful than others as expected considering reports of their rapid rate of genome evolution and the worst results were obtained for several arthropods. Some general patterns among phyla arose, and we discuss how the results of this EPIC survey may give new insights into genome evolution of the study species. This work confirms that this set of EPIC loci provides an easy-to-use toolbox to identify genetic markers potentially useful for population genetics, phylogeography or phylogenetic studies for a large panel of metazoan species. We then argue that obtaining diploid sequence genotypes for these loci became simple and affordable owing to Next-Generation Sequencing development. Species surveyed in this study belong to several genera (Acanthaster, Alvinocaris, Aplysina, Aurelia, Crepidula, Eunicella, Hediste, Hemimysis, Litoditis, Lophelia, Mesopodopsis, Mya, Ophiocten, Ophioderma, Ostrea, Pelagia, Platynereis, Rhizostoma, Rimicaris), two of them, belonging to the family Vesicomydae and Eunicidae, could not be determined at the genus level.

Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas

Crassostrea gigas originated from the Pacific coast of Asia, but was introduced into several European countries in the early 1970s. Natural populations have now spread across the length of the western seaboard of Europe. To elucidate the demographic and selective processes at play during this rapid expansion, genome-scan analysis was performed on different populations. High diversities and low differentiation were observed overall, but significant genetic differentiation was found among newly established populations and between the newly established northern group and a nearly panmictic group composed of southern European populations and a population from Japan. Loss of genetic diversity was also seen in the north, likely caused by founder events during colonization. The few strongly supported outlier loci revealed a genetic structure uncorrelated with the north/south differentiation, but grouping two samples from the Danish fjords (northern group) and one from the Dutch Scheldt estuary (southern group) with the one from Japan. These findings might reflect the following: (i) parallel adaptation to similar environmental pressures (fjord-like environment) within each of the two groups or (ii) a footprint of a secondary introduction of an alternative genomic background maintained by multifarious isolation factors. Our results call for a closer examination of adaptive genetic structure in the area of origin.

A high load of non-neutral amino-acid polymorphisms explains high protein diversity despite moderate effective population size in a marine bivalve with sweepstakes reproduction

Marine bivalves show among the greatest allozyme diversity ever reported in Eukaryotes, putting them historically at the heart of the neutralist-selectionist controversy on the maintenance of genetic variation. Although it is now acknowledged that this high diversity is most probably a simple consequence of a large population size, convincing support for this explanation would require a rigorous assessment of the silent nucleotide diversity in natural populations of marine bivalves, which has not yet been done. This study investigated DNA sequence polymorphism in a set of 37 nuclear loci in wild samples of the flat oyster Ostrea edulis. Silent diversity was found to be only moderate (0.7%), and there was no departure from demographic equilibrium under the Wright-Fisher model, suggesting that the effective population size might not be as large as might have been expected. In accordance with allozyme heterozygosity, nonsynonymous diversity was comparatively very high (0.3%), so that the nonsynonymous to silent diversity ratio reached a value rarely observed in any other organism. We estimated that one-quarter of amino acid-changing mutations behave as neutral in O. edulis, and as many as one-third are sufficiently weakly selected to segregate at low frequency in the polymorphism. Finally, we inferred that one oyster is expected to carry more than 4800 non-neutral alleles (or 4.2 cM(-1)). We conclude that a high load of segregating non-neutral amino-acid polymorphisms contributes to high protein diversity in O. edulis. The high fecundity of marine bivalves together with an unpredictable and highly variable success of reproduction and recruitment (sweepstakes reproduction) might produce a greater decoupling between Ne and N than in other organisms with lower fecundities, and we suggest this could explain why a higher segregating load could be maintained for a given silent mutation effective size.

Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification

BACKGROUND

Because of its typical architecture, inheritance and small size, mitochondrial (mt) DNA is widely used for phylogenetic studies. Gene order is generally conserved in most taxa although some groups show considerable variation. This is particularly true in the phylum Mollusca, especially in the Bivalvia. During the last few years, there have been significant increases in the number of complete mitochondrial sequences available. For bivalves, 35 complete mitochondrial genomes are now available in GenBank, a number that has more than doubled in the last three years, representing 6 families and 23 genera. In the current study, we determined the complete mtDNA sequence of O. edulis, the European flat oyster. We present an analysis of features of its gene content and genome organization in comparison with other Ostrea, Saccostrea and Crassostrea species.

RESULTS

The Ostrea edulis mt genome is 16 320 bp in length and codes for 37 genes (12 protein-coding genes, 2 rRNAs and 23 tRNAs) on the same strand. As in other Ostreidae, O. edulis mt genome contains a split of the rrnL gene and a duplication of trnM. The tRNA gene set of O. edulis, Ostrea denselamellosa and Crassostrea virginica are identical in having 23 tRNA genes, in contrast to Asian oysters, which have 25 tRNA genes (except for C. ariakensis with 24). O. edulis and O. denselamellosa share the same gene order, but differ from other Ostreidae and are closer to Crassostrea than to Saccostrea. Phylogenetic analyses reinforce the taxonomic classification of the 3 families Ostreidae, Mytilidae and Pectinidae. Within the Ostreidae family the results also reveal a closer relationship between Ostrea and Saccostrea than between Ostrea and Crassostrea.

CONCLUSIONS

Ostrea edulis mitogenomic analyses show a high level of conservation within the genus Ostrea, whereas they show a high level of variation within the Ostreidae family. These features provide useful information for further evolutionary analysis of oyster mitogenomes.

QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas)

Summer mortality is a phenomenon severely affecting the aquaculture production of the Pacific oyster (Crassostrea gigas). Although its causal factors are complex, resistance to mortality has been described as a highly heritable trait, and several pathogens including the virus Ostreid Herpes virus type 1 (OsHV-1) have been associated with this phenomenon. A QTL analysis for survival of summer mortality and OsHV-1 load, estimated using real-time PCR, was performed using five F(2) full-sib families resulting from a divergent selection experiment for resistance to summer mortality. A consensus linkage map was built using 29 SNPs and 51 microsatellite markers. Five significant QTL were identified and assigned to linkage groups V, VI, VII and IX. Analysis of single full-sib families revealed differential QTL segregation between families. QTL for the two-recorded traits presented very similar locations, highlighting the interest of further study of their respective genetic controls. These QTL show substantial genetic variation in resistance to summer mortality, and present new opportunities for selection for resistance to OsHV-1.

Mitochondrial and nuclear DNA analysis of genetic heterogeneity among recruitment cohorts of the European flat oyster Ostrea edulis

Marine species with high fecundity and high early mortality may also have high variance in reproductive success among individuals due to stochastic factors, making successful reproduction a "sweepstakes." In some cases, the impact is sufficient to reduce the effective number of breeders in wild populations. We tested two predictions of the sweepstakes reproductive success hypothesis in a French Atlantic population of the European flat oyster, Ostrea edulis, by evaluating (1) whether individuals belonging to temporally discrete recruitment cohorts within a single reproductive season displayed reduced genetic variation relative to the entire adult population, and (2) whether these temporal cohorts of recruits were genetically differentiated from each other. We assayed genetic variation at four nuclear microsatellites and a 12S mitochondrial fragment in four recruitment cohorts. Nuclear markers provided no evidence for differentiation between recruitment cohorts and adults or between temporal cohorts. However, mitochondrial data indicate that the first temporal cohort showed significant differentiation with the last (Fst = 0.052, P < 0.05) and with the adult sample (Fst = 0.058, P < 0.05). These differences are most likely due to the smaller effective size of the mitochondrial genome-and hence its increased sensitivity to drift compared to the nuclear genome. This slight mitochondrial signal indicates a certain limitation in the number of contributing female parents in this species. The "sweepstakes" phenomenon was therefore limited in our case. Hypothetically, this phenomenon may occur or not, with a high variance as a result of the interaction between the oyster reproductive biology and different environmental conditions.

Combining two-stage testing and interval mapping strategies to detect QTL for resistance to bonamiosis in the european flat oyster Ostrea edulis

We have identified quantitative trait loci (QTL) in the flat oyster (Ostrea edulis) for resistance to Bonamia ostreae, a parasite responsible for the dramatic reduction in the aquaculture of this species. An F(2) family from a cross between a wild oyster and an individual from a family selected for resistance to bonamiosis was cultured with wild oysters injected with the parasite, leading to 20% cumulative mortality. Selective genotyping of 92 out of a total of 550 F(2) progeny (i.e., 46 heavily infected oysters that died and 46 parasite-free oysters that survived) was performed using 20 microsatellites and 34 amplification fragment length polymorphism primer pairs. Both a two-stage testing strategy and QTL interval mapping methods were used. The two-stage detection strategy had a high power with a low rate of false positives and identified nine and six probable markers linked to genes of resistance and susceptibility, respectively. Parent-specific genetic linkage maps were built for the family, spanning ten linkage groups (n = 10) with an observed genome coverage of 69-84%. Three QTL were identified by interval mapping in the first parental map and two in the second. Good concordance was observed between the results obtained after the two-stage testing strategy and QTL mapping.

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase

BACKGROUND

Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available.

DESCRIPTION

In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster.

CONCLUSION

A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Detection of phenoloxidase activity in early stages of the Pacific oyster Crassostrea gigas (Thunberg)

The presence of phenoloxidase (PO) activity was detected in different developmental stages of the Pacific oyster, Crassostrea gigas. A significant reduction in PO activity was observed from the 6h embryo stage to the day 11 larvae by spectrophotometry. A progressive increase was also observed from the day 13 larvae right through to the juvenile stage. The microscopy studies with '6h embryo' and adult samples confirmed the presence of PO activity. Various modulators of PO activity were used to study the triggering of pro-phenoloxidase (proPO) activating system of C. gigas but also to confirm the exact nature of the monitored activity. The enzyme activation mechanisms appear to differ with the developmental stage: bacterial lipopolysaccharides constitute an early elicitor of the proPO-PO system, whereas a purified trypsin triggers proPO-PO system in C. gigas spat. Phenoloxidase activity was totally suppressed by PO-specific inhibitors such as beta-2-mercaptoethanol, sodium diethyldithiocarbonate and tropolone. This study demonstrated the selective response of PO-like activity by different elicitors and suggested that proPO-PO activating system, which is supposed to play an important function in non-self recognition and host immune reactions in oyster, is expressed early in the Pacific oyster, C. gigas.

Characterization of 27 microsatellite loci in the European flat oyster Ostrea edulis

The flat oyster Ostrea edulis is native to Europe and populations have been severely depleted by the parasite Bonamia ostreae since the 1980s. Additional genetic markers are required to improve population genetics study and linkage map development for selection for B. ostrea-resistance in this species. Here, we characterized 27 novel microsatellite loci for O. edulis. Number of alleles per locus ranged from 6 to 25 and observed heterozygosity between 0.375 and 1. Null alleles were suggested at a few loci but most loci were in Hardy-Weinberg agreement enabling their reliable use in further population and mapping genetics approaches.

Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas

DNA sequence polymorphism and codon usage bias were investigated in a set of 41 nuclear loci in the Pacific oyster Crassostrea gigas. Our results revealed a very high level of DNA polymorphism in oysters, in the order of magnitude of the highest levels reported in animals to date. A total of 290 single nucleotide polymorphisms (SNPs) were detected, 76 of which being localised in exons and 214 in non-coding regions. Average density of SNPs was estimated to be one SNP every 60 bp in coding regions and one every 40 bp in non-coding regions. Non-synonymous substitutions contributed substantially to the polymorphism observed in coding regions. The non-synonymous to silent diversity ratio was 0.16 on average, which is fairly higher to the ratio reported in other invertebrate species recognised to display large population sizes. Therefore, purifying selection does not appear to be as strong as it could have been expected for a species with a large effective population size. The level of non-synonymous diversity varied greatly from one gene to another, in accordance with varying selective constraints. We examined codon usage bias and its relationship with DNA polymorphism. The table of optimal codons was deduced from the analysis of an EST dataset, using EST counts as a rough assessment of gene expression. As recently observed in some other taxa, we found a strong and significant negative relationship between codon bias and non-synonymous diversity suggesting correlated selective constraints on synonymous and non-synonymous substitutions. Codon bias as measured by the frequency of optimal codons for expression might therefore provide a useful indicator of the level of constraint upon proteins in the oyster genome.

AFLP-based genetic linkage maps of the blue mussel (Mytilus edulis)

We report the construction of the first genetic linkage map in the blue mussel, Mytilus edulis. AFLP markers were used in 86 full-sib progeny from a controlled pair mating, applying a double pseudo-test cross strategy. Thirty-six primer pairs generated 2354 peaks, of which 791 (33.6%) were polymorphic in the mapping family. Among those, 341 segregated through the female parent, 296 through the male parent (type 1:1) and 154 through both parents (type 3:1). Chi-square goodness-of-fit tests revealed that 71% and 73% of type 1:1 and 3:1 markers respectively segregated according to Mendelian inheritance. Sex-specific linkage maps were built with mapmaker 3.0 software. The female framework map consisted of 121 markers ordered into 14 linkage groups, spanning 862.8 cM, with an average marker spacing of 8.0 cM. The male framework map consisted of 116 markers ordered into 14 linkage groups, spanning 825.2 cM, with an average marker spacing of 8.09 cM. Genome coverage was estimated to be 76.7% and 75.9% for the female and male framework maps respectively, rising to 85.8% (female) and 86.2% (male) when associated markers were included. Twelve probable homologous linkage group pairs were identified and a consensus map was built for nine of these homologous pairs based on multiple and parallel linkages of 3:1 markers, spanning 816 cM, with joinmap 4.0 software.

Impact of diuron on aneuploidy and hemocyte parameters in Pacific oyster, Crassostrea gigas

Diuron is a substituted urea herbicide used for agricultural and nonagricultural weed control. Its widespread use and relatively slow breakdown led us to analyze its influence on aneuploidy level (lowered chromosome number in a percentage of somatic cells) and hemocyte parameters in Pacific oysters, Crassostrea gigas. Adult oysters were subjected to two diuron concentrations (300 ng L(-1) and 3 microg L(-1)) for 11 weeks. Significantly higher aneuploidy level was observed in diuron-treated oysters compared with the control. Furthermore, the observed impact on aneuploidy persisted to the next generation as offspring exhibited significantly higher aneuploidy levels when their parents had been exposed to diuron. Significant increases in hemocyte parameters (cell mortality, phagocytosis, granulocyte percentage, reactive oxygen species, and lysosome presence) of the adults were also observed after 4 weeks of diuron exposure. The effects observed on oyster aneuploidy level and hemocyte parameters could have serious environmental and practical consequences.

Phylogeography of the green turtle, Chelonia mydas, in the Southwest Indian Ocean

Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.

Effects of cadmium on aneuploidy and hemocyte parameters in the Pacific oyster, Crassostrea gigas

Pacific oysters, Crassostrea gigas, are commonly reared in estuaries where they are exposed to anthropogenic pollution. Much research has been made on the toxicity of cadmium to aquatic organisms because the compound recurrently contaminates their environment. Our study examined the influence of cadmium on aneuploidy level (lowered chromosome number in a percentage of somatic cells) and hemocyte parameters in C. gigas at different stages of life. Adults and juveniles were exposed to two different concentrations of cadmium. The first concentration applied was equivalent to a peak value found in Marennes-Oléron bay (Charente-Maritime, France; 50 ngL(-1)) and the second was 10 times higher (500 ngL(-1)). Exposure to 50 ngL(-1) cadmium caused a significant decrease in the survival time of C. gigas, but exposure to 500 ngL(-1) surprisingly affected the survival time positively. Significant differences in aneuploidy level were observed between the cadmium treatments and the control in adults but not in juveniles or the offspring of the adult groups. The effects of cadmium on hemocyte parameters were analyzed by flow cytometry. Several hemocyte parameters increased significantly after 21 days of cadmium exposure and subsequently decreased. Phenoloxidase-like activity, evaluated by spectrophotometry, varied over the time of the experiment and increased after 66 days of contact with 500 ngL(-1) cadmium. Taken together, cadmium at environmentally relevant concentrations seems to have only moderate effects on aneuploidy and hemocyte parameters.

Endonuclease banding reveals that atrazine-induced aneuploidy resembles spontaneous chromosome loss in Crassostrea gigas

Aneuploidy has previously been observed in the Pacific oyster, Crassostrea gigas, and shown to be negatively correlated with growth. Moreover, a significant impact of atrazine exposure has been described in C. gigas, and persistence of that effect has been observed between generations. Evidence of differential chromosome loss has been demonstrated in aneuploid karyotypes of C. gigas using the G-banding technique. Pairs 1, 5, 9, and 10 are characterized by the loss of 1 chromosome. As restriction enzyme (RE) digestion chromosome banding allows a better identification of chromosome pairs, we used this technique to identify which chromosomes are affected when aneuploidy is increased by exposure to atrazine. The progeny of oysters contaminated by atrazine were analysed using the restriction enzyme HaeIII. The study of 26 RE-banded aneuploid karyotypes showed that the same chromosome pairs (1, 5, 9, and 10) were affected by the loss of 1 chromosome (61%, 15%, 42%, and 42%, respectively). Further investigation is required to enable a better understanding of aneuploidy in oysters, especially with respect to why some chromosomes are more easily lost than others, and why cells tolerate the loss of these chromosomes.

A complementary method for production of tetraploid Crassostrea gigas using crosses between diploids and tetraploids with cytochalasin b treatments

We present a new method to produce tetraploid Crassostrea gigas by cytochalasin B inhibition of polar body 2 expulsion in diploid females crossed with tetraploid males. This offers a means of direct introgression of genetic characters from selected diploid to tetraploid lines, avoiding a triploid step. Offspring larval ploidy shifted over time and depended on size, with tetraploids more frequent among the smaller larvae and triploids among the large. Viable tetraploids were found at 4 and 6 months, indicating the technique was successful. The possibility that gynogenesis occurred was tested by microsatellite analysis to confirm the presence of paternally inherited alleles. These were present in all animals of the 2n x 4n + CB (female first) cross. However, a 4n x 2n + CB cross produced triploids, including some gynogens. Our method illustrates for the first time that diploid C. gigas eggs, if selected for large size, can give viable tetraploid offspring.

Reduced female gene flow in the European flat oyster Ostrea edulis

The geographical structure of 15 natural populations of the flat oyster (Ostrea edulis L.) was assessed by single-strand conformation polymorphism (SSCP) of a 313-base-pair (bp) fragment of the mitochondrial 12S-rRNA gene. Fourteen haplotypes were observed, with one being dominant in the Mediterranean samples and another one in the Atlantic populations. The geographically extreme populations sampled in Norway and the Black Sea appeared differentiated by exhibiting the dominance of a third group of haplotypes. The results were compared to available microsatellite data at five loci. The Atlantic/Mediterranean differentiation pattern was qualitatively the same with both types of markers, confirming an isolation-by-distance pattern. The average mitochondrial haplotypic diversity displayed a high among populations variance, reflecting small effective population size in some locations. Additionally, a 10-fold quantitative difference was observed in Fst between the mitochondrial and the nuclear genomes, which could be due to an unbalanced sex ratio or sex-biased differential reproductive success between males and females (or both).

Impact of atrazine on aneuploidy in pacific oysters, Crassostrea gigas

Aneuploidy has previously been described and studied in the Pacific oyster, Crassostrea gigas, and has been shown to be negatively correlated with growth. The present study investigated the effect of atrazine on the level of aneuploidy in this species. Crassostrea gigas adults and juveniles were subjected to different concentrations of atrazine representing a peak value found in a polluted environment (46.5 nM) and a value 10 times higher (465 nM). Although atrazine did not show any effect on the oyster mortality, significant differences in aneuploidy level were observed between the different treatments (9% for the control, 16% for 46.5 nM and 20% for 465 nM atrazine). Moreover, the same levels of aneuploidy were observed at adult and juvenile stages. This is the first reported evidence for an environmental effect on aneuploidy in C. gigas. These results will be useful for the oyster aquaculture industry and management of resources. The lowest atrazine level in the current study represents realistic potential exposure, and the results suggest that studies should be made on other aquatic species at risk of exposure to atrazine in the wild. This widely used compound may be an important factor causing damage to genetic material.

Trans-atlantic distribution of a mangrove oyster species revealed by 16S mtDNA and karyological analyses

Three species of mangrove oysters, Crassostrea rhizophorae, C. brasiliana, and C. gasar, have been described along the Atlantic shores of South America and Africa. Because the distribution of these molluscs is of great biological and commercial interest, their taxonomy and distribution deserve further clarification. Therefore, 15 populations were sampled from both continents. Their 16S mitochondrial polymorphism was studied by sequencing and PCR-RFLP analysis. Two haplotypes were identified. Haplotype a was the only one observed in Africa, but it was also observed in South America together with haplotype b. Because C. gasar is the only mangrove oyster identified on the west coast of Africa, haplotype a was attributed to this species, which has thus been shown to occur in South America. Haplotype b is attributed to C. rhizophorae. The karyotypes of specimens of C. gasar, from Africa and from South America, were very similar, and both species were observed at the same location in Brazil. The occurrence of C. gasar in South America adds a third species-in addition to C. rhizophorae and C. brasiliana-to the list of species present along these coasts. The predominant surface circulation patterns in this part of the Atlantic Ocean favor the hypothesis that C. gasar was transported from Africa to America. Finally, a phylogenetic tree built with seven 16S sequences from Crassostrea and Saccostrea species showed that C. gasar is intermediate between the American Crassostrea species (C. virginica and C. rhizophorae) and the Asian species (C. gigas and C. ariakensis).