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

Artigaud, Sébastien; Thorne, Michael A. S.; Richard, Joëlle; Lavaud, Romain; Jean, Fred; Flye-Sainte-Marie, Jonathan; Peck, Lloyd S.; Pichereau, Vianney; Clark, Melody S.

doi:10.1016/j.margen.2014.03.006

Cited by 46 publications

(32 citation statements)

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“…Gene sequences were predicted using Augustus annotation software [46], with one novel (K. James, available for download from Figshare link, see data sources section) and several previously published P. maximus RNAseq datasets [47,48] used for training. The non-masked genome was used as the basis for gene prediction, to avoid artefacts, missed exons or missing gene portions caused by gene overlap with masked areas of the genome.…”

Section: Gene Prediction and Annotationmentioning

confidence: 99%

The Gene-Rich Genome of the ScallopPecten maximus

Kenny

McCarthy

Dudchenko

et al. 2020

Preprint

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AbstractBackgroundThe 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 its ubiquity means that it 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.FindingsHere we report the genome sequencing 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, and 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.ConclusionsThe genome assembly of Pecten maximus and its annotated gene set provide a high-quality platform for a wide range of investigations, including 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 as a gene conferring resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

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Section: Gene Prediction and Annotationmentioning

confidence: 99%

The Gene-Rich Genome of the ScallopPecten maximus

Kenny

McCarthy

Dudchenko

et al. 2020

Preprint

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“…The mantle tissue of mollusks has multiple functions, which include ligament secretion and sensorial activities; moreover, this tissue is very responsive to external stimuli (Artigaud et al, 2015). The mantle tissue has been used for transcriptome, proteomic, or metabolomic analyses in many studies (Artigaud et al, 2014(Artigaud et al, , 2015Wei et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics

Jiang

Jiao

Sun

et al. 2020

PeerJ

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Marine mollusks are commonly subjected to heat stress. To evaluate the effects of heat stress on the physiological metabolism of the ark shell Scapharca subcrenata, clams were exposed to different high temperatures (24, 28 and 32 °C) for 72 h. The oxygen consumption and ammonia excretion rates were measured at 2, 12, 24, 48 and 72 h. The results indicated that the metabolic rates of the ark shell significantly increased with increasing heat stress, accompanied by mortalities in response to prolonged exposure. A metabolomics approach based on gas chromatography coupled with mass spectrometry was further applied to assess the changes of metabolites in the mantle of the ark shell at 32 °C. Moreover, multivariate and pathway analyses were conducted for the different metabolites. The results showed that the heat stress caused changes in energy metabolism, amino acid metabolism, osmotic regulation, carbohydrate metabolism and lipid metabolism through different metabolic pathways. These results are consistent with the significant changes of oxygen consumption rate and ammonia excretion rate. The present study contributes to the understanding of the impacts of heat stress on intertidal bivalves and elucidates the relationship between individual-level responses and underlying molecular metabolic dynamics.

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“…A number of recent papers have focused on the characterization of biomineralization proteins and genes in mollusks (Gardner et al, 2011;Jackson et al, 2010;Joubert et al, 2010;Shi et al, 2012;Zhang and Zhang, 2006;Zhao et al, 2012a), while other studies have increased the number of available molluscan transcriptomes to include pearl oysters Zhao et al, 2012aZhao et al, , 2012b, sea hares (Fiedler et al, 2010;Heyland et al, 2011), freshwater snails (Sadamoto et al, 2012), abalone (Franchini et al, 2011;Picone et al, 2015), scallops (Artigaud et al, 2014), mussels (Freer et al, 2014), and clams (Clark et al, 2010;Sleight et al, 2015). These studies confirm that molluscan biomineralization is a complex process with some conserved pathways shared between distantly related animal groups, and other proteins and compounds that are taxonomically restricted (Jackson et al, 2010), as has been shown in more distantly related animal groups (Jackson et al, 2007;Moya et al, 2008Moya et al, , 2012.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-wide analysis of the response of the thecosome pteropod Clio pyramidata to short-term CO2 exposure

Maas

Lawson

Tarrant

2015

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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12Thecosome pteropods, a group of calcifying holoplanktonic molluscs, have recently become a 13 research focus due to their potential sensitivity to increased levels of anthropogenic dissolved 14 CO2 in seawater and the accompanying ocean acidification. Some populations, however, already 15 experience high CO2 in their natural distribution during diel vertical migrations. To achieve a 16 better understanding of the mechanisms of pteropod calcification and physiological response to 17 this sort of short duration CO2 exposure, we characterized the gene complement of Clio 18 pyramidata, a cosmopolitan diel migratory thecosome, and investigated its transcriptomic 19 response to experimentally manipulated CO2 conditions. Individuals were sampled from the 20 Northwest Atlantic in the fall of 2011 and exposed to ambient conditions (~380 ppm) and 21 elevated CO2 (~800 ppm, similar to levels experienced during a diel vertical migration) for ~10 Introduction 50The dissolution of anthropogenic carbon dioxide (CO2) into seawater, or ocean acidification 51 (OA), stands to impact a broad variety of marine organisms, especially those that secrete calcium 52 carbonate (CaCO3) shells or skeletons (Fabry et al., 2008). As CO2 equilibrates into seawater, pH 53 and the concentration of carbonate ions decrease, causing CaCO3 to dissociate and affecting the 54 ability of calcifying animals to create and maintain calcareous structures (Gattuso et al., 1999; 55 Riebesell et al., 2000). Furthermore, decreasing pH in the water alters the acid-base balance of 56 the intra-and extracellular fluids of marine organisms (Miles et al., 2007; Seibel and Fabry, 57 2003; Seibel and Walsh, 2001). Since CO2 is produced naturally as a byproduct of respiration, all 58 organisms have physiological mechanisms for maintaining internal cellular pH. These 59 compensatory mechanisms may, however, cease to function if internal acidosis becomes too 60 severe over short time scales and generally fail over extended periods of internal pH imbalance. 61Classical organismal-level metrics (e.g., metabolic rate, calcification, mortality) have revealed a 62 complex pattern of intra-and inter-specific variation in responses to CO2 exposure (reviewed in 63 Hendriks et al., 2010; Kroeker et al., 2013; Kroeker et al., 2010). The variability in these 64 responses, and their dependence on duration of exposure or co-varying stressors, suggest that 65 there is an energetic cost associated with compensating for high CO2 (e.g., 662011; Langenbuch and Pörtner, 2004; Stumpp et al., 2011b). 68Cummings et al., One group thought to be particularly sensitive to OA is the thecosomatous (i.e., shelled) 71 pteropods. These holoplanktonic gastropods, related to terrestrial snails and also known as sea 72 butterflies, produce thin shells made of aragonite, a highly soluble form of CaCO3. In temperate 73 and polar seas, thecosomes can become a numerically dominant member of the zooplankton 74 community (Hunt et al., 2008). This causes them to be significant consum...

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

Cited by 46 publications

References 14 publications

The Gene-Rich Genome of the ScallopPecten maximus

The Gene-Rich Genome of the ScallopPecten maximus

Metabolic response of Scapharca subcrenata to heat stress using GC/MS-based metabolomics

Transcriptome-wide analysis of the response of the thecosome pteropod Clio pyramidata to short-term CO2 exposure

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