The gene-rich genome of the scallop Pecten maximus

BACKGROUND

The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management.

FINDINGS

Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species.

CONCLUSIONS

The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

Transcriptomic features of Pecten maximus oocyte quality and maturation

The king scallop Pecten maximus is a high valuable species of great interest in Europe for both fishery and aquaculture. Notably, there has been an increased investment to produce seed for enhancement programmes of wild scallop populations. However, hatchery production is a relatively new industry and it is still underdeveloped. Major hurdles are spawning control and gamete quality. In the present study, a total of 14 scallops were sampled in the bay of Brest (Brittany, France) to compare transcriptomic profiles of mature oocytes collected by spawning induction or by stripping. To reach such a goal, a microarray analysis was performed by using a custom 8x60K oligonucleotide microarray representing 45,488 unique scallop contigs. First we identified genes that were differentially expressed depending on oocyte quality, estimated as the potential to produce D-larvae. Secondly, we investigated the transcriptional features of both stripped and spawned oocytes. Genes coding for proteins involved in cytoskeletal dynamics, serine/threonine kinases signalling pathway, mRNA processing, response to DNA damage, apoptosis and cell-cycle appeared to be of crucial importance for both oocyte maturation and developmental competence. This study allowed us to dramatically increase the knowledge about transcriptional features of oocyte quality and maturation, as well as to propose for the first time putative molecular markers to solve a major bottleneck in scallop aquaculture.

Characterization of the mantle transcriptome in bivalves: Pecten maximus, Mytilus edulis and Crassostrea gigas

The calcareous shells secreted by bivalve molluscs display diverse and species specific structural compositions, which indicates possible divergent biomineralization processes. Thus, studying multiple mollusc species will provide a more comprehensive understanding of shell formation. Here, the transcriptomes of the mantle tissues responsible for shell deposition were characterized in three commercially relevant bivalve species. Using high-throughput sequencing and bioinformatics tools, de novo transcriptome assemblies of mantle tissues were generated for the mussel Mytilus edulis, the oyster Crassostrea gigas and the scallop Pecten maximus. These transcriptomes were annotated, and contigs with similarity to proteins known to have shell formation roles in other species were identified. Comparison of the shell formation specific proteins in the three bivalves indicates the possibility of species specific shell proteins.

Deep sequencing of the mantle transcriptome of the great scallop Pecten maximus

RNA-Seq transcriptome data were generated from mantle tissue of the great scallop, Pecten maximus. The consensus data were produced from a time course series of animals subjected to a 56-day thermal challenge at 3 different temperatures. A total of 26,064 contigs were assembled de novo, providing a useful resource for both the aquaculture community and researchers with an interest in mollusc shell production.

Deep transcriptome sequencing of Pecten maximus hemocytes: a genomic resource for bivalve immunology

Pecten maximus, the king scallop, is a bivalve species with important commercial value for both fisheries and aquaculture, traditionally consumed in several European countries. Major problems in larval rearing, however, still limit hatchery-based seed production. High mortalities during early larval stages, likely related to bacterial pathogens, represent the most relevant bottleneck. To address this issue, understanding host defense mechanisms against microbes is extremely important. In this study next-generation RNA-sequencing was carried on scallop hemocytes. To enrich for immune-related transcripts, cDNA libraries from hemocytes challenged in vivo with inactivated-Vibrio anguillarum and in vitro with pathogen-associated molecular patterns, as well as unchallenged controls, were sequenced yielding 216,444,674 sequence reads. De novo assembly of the scallop hemocyte transcriptome consisted of 73,732 contigs (31% annotated). A total of 934 contigs encoded proteins with a known immune function, grouped into several functional categories. Particular attention was reserved to Toll-like receptors (TLRs), a family of pattern recognition receptors (PRRs) involved in non-self recognition. Through mining the scallop hemocyte transcriptome, at least four TLRs could be identified. The organization of canonical TLR domains demonstrated that single cysteine cluster and multiple cysteine cluster TLRs co-exist in this species. In addition, preliminary data concerning their mRNA level following bacterial challenge suggested that different members of this family could exhibit opposite responses to pathogenic stimuli. Finally, a global analysis of differential expression comparing gene-expression levels in in vitro and in vivo stimulated hemocytes against controls provided evidence on a large set of transcripts involved in the great scallop immune response.

Karyotype and Chromosomal Location of 18S–28S and 5S Ribosomal DNA in the Scallops Pecten maximus and Mimachlamys varia (Bivalvia: Pectinidae)

This work describes the karyotype and chromosomal location of the ribosomal DNA (rDNA) of Pecten maximus and Mimachlamys varia, two commercial scallop species from Europe. According to the chromosome centromeric index values found, the karyotype of P. maximus is composed of 1 metacentric, 2 metacentric-submetacentric, 1 telocentric-subtelocentric and 15 telocentric pairs, and that of M. varia of 4 metacentric, 2 subtelocentric-submetacentric, 9 subtelocentric, 3 subtelocentric-telocentric and 1 telocentric-subtelocentric pairs. In P. maximus, 18S-28S rDNA was located by FISH on a metacentric-submetacentric pair, and in M. varia on a subtelocentric-submetacentric pair using both silver staining and FISH. PCR amplification of the 5S rDNA unit yielded a single product of about 460 bp (P. maximus) and 450 bp (M. varia), that used as probe revealed a 5S rDNA site on a telocentric pair in P. maximus and a subtelocentric pair in M. varia. Two-color FISH or sequential silver staining of 5S rDNA-FISH-metaphases corroborated that the two gene families are located on different chromosomes in both species. A comparative analysis of the data allowed the inference of karyotypic relationships within scallops.

Identification of Mytilus spp. and Pecten maximus in Irish waters by standard PCR of the 18S rDNA gene and multiplex PCR of the 16S rDNA gene

Two molecular protocols for the identification of mussel and scallop have been developed using specific primers targeting the mitochondrial 16S ribosomal DNA gene and the nuclear 18S ribosomal DNA gene. Primers for the mitochondrial 16S ribosomal DNA gene in multiplex polymerase chain reaction (PCR) protocols yielded diagnostic DNA fragments for the mussels Mytilus edulis, Mytilus galloprovincialis, and the hybrid Mytilus edulis/galloprovincialis (335 bp), the king scallop Pecten maximus (382 bp) and the black scallop Mimachlamys varia (398 bp). DNA from the queen scallop Aequipecten opercularis showed no consistent PCR amplification of the 16S rDNA gene. Primers for the nuclear 18S rDNA gene in standard PCR protocols yielded similar-sized, diagnostic DNA fragments (approx. 190 bp) for the mussels Mytilus edulis, Mytilus galloprovincialis, and the hybrid Mytilus edulis/galloprovincialis, the king scallop Pecten maximus, the black scallop Mimachlamys varia, and the queen scallop Aequipecten opercularis. Both protocols have been tested with Mytilus spp., P. maximus, and 6 other bivalve species from a wide range of locations in Irish and European waters. Cross reaction of the specific primers with DNA template from any of the 6 other bivalve species was not observed. Rapid DNA extraction using FTA Card technology and the16S rDNA primers allowed for the detection of at least 10 mussel larvae in a subsample of natural plankton.