The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas

AbstractThe Pacific oyster Crassostrea gigas is an important cultivated shellfish. As a euryhaline species, it has evolved adaptive mechanisms responding to the complex and changeable intertidal environment that it inhabits. To investigate the genetic basis of this salinity adaptation mechanism, we conducted a genome-wide association study using phenotypically differentiated populations (hyposalinity and hypersalinity adaptation populations, and control population), and confirmed our results using an independent population, high-resolution melting, and mRNA expression analysis. For the hyposalinity adaptation, we determined 24 genes, including Cg_CLCN7 (chloride channel protein 7) and Cg_AP1 (apoptosis 1 inhibitor), involved in the ion/water channel and transporter mechanisms, free amino acid and reactive oxygen species metabolism, immune responses, and chemical defence. Three SNPs located on these two genes were significantly differentiated between groups, as was Cg_CLCN7. For the hypersalinity adaptation, the biological process for positive regulating the developmental process was enriched. Enriched gene functions were focused on transcriptional regulation, signal transduction, and cell growth and differentiation, including calmodulin (Cg_CaM) and ficolin-2 (Cg_FCN2). These genes and polymorphisms possibly play an important role in oyster hyposalinity and hypersalinity adaptation. They not only further our understanding of salinity adaptation mechanisms but also provide markers for highly adaptable oyster strains suitable for breeding.</jats:p

Development of single nucleotide polymorphisms in key genes of taurine and betaine metabolism in Crassostrea hongkongensis and their association with content-related traits

Abstract Background Taurine and betaine are important nutrients in the Hong Kong oyster (Crassostrea hongkongensis) and have many important biological properties. To investigate the characteristics of taurine and betaine and identify single nucleotide polymorphisms (SNPs) associated with traits in C. hongkongensis, we cloned the full-length cDNA of key genes involved in taurine and betaine metabolism (unpublished data), determined taurine and betaine content and gene expression in different tissues and months of the oyster specimen collection, and developed SNPs in the gene coding region. Results We cloned the full-length cDNA of the genes that express cysteine dioxygenase and cysteine sulfite decarboxylase (ChCSAD and ChCDO, respectively), which are key genes involved in taurine metabolism in C. hongkongensis, and found that betaine and taurine contents and the expression of key genes were regulated by seawater salinity. A total of 47 SNP markers were developed in the coding regions of ChCSAD, ChCDO, choline dehydrogenase (ChCDH), betaine aldehyde dehydrogenase (ChBADH), and betaine homocysteine methyltransferase (ChBHMT) using gene fragment resequencing and FLDAS-PCR. Through association analysis of a population of C. hongkongensis in the Maowei Sea, Guangxi, nine SNPs were found to be associated with taurine content, and one SNP was associated with betaine content. Haploid and linkage disequilibrium analyses showed that SNPs in ChCDO formed one linkage group with three haplotypes: ACACA, GTACA and GTTTG. The average taurine content of the corresponding individuals was 873.88, 838.99, and 930.72 μg/g, respectively, indicating the GTTTG haplotype has a significant advantage in terms of taurine content. Conclusions SNPs associated with taurine and betaine contents in C. hongkongensis were identified for the first time. We found that the GTTTG haplotype in the ChCDO coding region has a significant advantage in taurine content. These loci and haplotypes can serve as potential molecular markers for the molecular breeding of C. hongkongensis

Genome and transcriptome analyses provide insight into the euryhaline adaptation mechanism of Crassostrea gigas.

BACKGROUND: The Pacific oyster, Crassostrea gigas, has developed special mechanisms to regulate its osmotic balance to adapt to fluctuations of salinities in coastal zones. To understand the oyster's euryhaline adaptation, we analyzed salt stress effectors metabolism pathways under different salinities (salt 5, 10, 15, 20, 25, 30 and 40 for 7 days) using transcriptome data, physiology experiment and quantitative real-time PCR. RESULTS: Transcriptome data uncovered 189, 480, 207 and 80 marker genes for monitoring physiology status of oysters and the environment conditions. Three known salt stress effectors (involving ion channels, aquaporins and free amino acids) were examined. The analysis of ion channels and aquaporins indicated that 7 days long-term salt stress inhibited voltage-gated Na(+)/K(+) channel and aquaporin but increased calcium-activated K(+) channel and Ca(2+) channel. As the most important category of osmotic stress effector, we analyzed the oyster FAAs metabolism pathways (including taurine, glycine, alanine, beta-alanine, proline and arginine) and explained FAAs functional mechanism for oyster low salinity adaptation. FAAs metabolism key enzyme genes displayed expression differentiation in low salinity adapted individuals comparing with control which further indicated that FAAs played important roles for oyster salinity adaptation. A global metabolic pathway analysis (iPath) of oyster expanded genes displayed a co-expansion of FAAs metabolism in C. gigas compared with seven other species, suggesting oyster's powerful ability regarding FAAs metabolism, allowing it to adapt to fluctuating salinities, which may be one important mechanism underlying euryhaline adaption in oyster. Additionally, using transcriptome data analysis, we uncovered salt stress transduction networks in C. gigas. CONCLUSIONS: Our results represented oyster salt stress effectors functional mechanisms under salt stress conditions and explained the expansion of FAAs metabolism pathways as the most important effectors for oyster euryhaline adaptation. This study was the first to explain oyster euryhaline adaptation at a genome-wide scale in C. gigas

The distribution of SNPs for each resequenced gene.

<p>The distribution of SNPs for each resequenced gene.</p

Candidate Gene Polymorphisms and their Association with Glycogen Content in the Pacific Oyster <i>Crassostrea gigas</i>

<div><p>Background</p><p>The Pacific oyster <i>Crassostrea gigas</i> is an important cultivated shellfish that is rich in nutrients. It contains high levels of glycogen, which is of high nutritional value. To investigate the genetic basis of this high glycogen content and its variation, we conducted a candidate gene association analysis using a wild population, and confirmed our results using an independent population, via targeted gene resequencing and mRNA expression analysis.</p><p>Results</p><p>We validated 295 SNPs in the 90 candidate genes surveyed for association with glycogen content, 86 of were ultimately genotyped in all 144 experimental individuals from Jiaonan (JN). In addition, 732 SNPs were genotyped via targeted gene resequencing. Two SNPs (Cg_SNP_TY202 and Cg_SNP_3021) in <i>Cg_GD1</i> (glycogen debranching enzyme) and one SNP (Cg_SNP_4) in <i>Cg_GP1</i> (glycogen phosphorylase) were identified as being associated with glycogen content. The glycogen content of individuals with genotypes TT and TC in Cg_SNP_TY202 was higher than that of individuals with genotype CC. The transcript abundance of both glycogen-associated genes was differentially expressed in high glycogen content and low glycogen content individuals.</p><p>Conclusions</p><p>This study identified three polymorphisms in two genes associated with oyster glycogen content, via candidate gene association analysis. The transcript abundance differences in <i>Cg_GD1</i> and <i>Cg_GP1</i> between low- and the high-glycogen content individuals suggests that it is possible that transcript regulation is mediated by variations of Cg_SNP_TY202, Cg_SNP_3021, and Cg_SNP_4. These findings will not only provide insights into the genetic basis of oyster quality, but also promote research into the molecular breeding of oysters.</p></div

The mRNA expression levels of the high glycogen content and the low glycogen content groups.

<p>* P < 0.05, the difference between the high glycogen content and the low glycogen content group of <i>Cg_GD1</i> was significant. <i>Cg_GD1</i>, glycogen debranching enzyme encoding gene 1. <i>Cg_GP1</i>, glycogen phosphorylase encoding gene 1.</p

Quantile-quantile plot for glycogen content.

<p>Quantile-quantile plot for glycogen content.</p

A Manhattan plot showing the associations of all SNPs.

<p>A Manhattan plot showing the associations of all SNPs.</p