Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

Comparative Methylome Analysis Reveals Epigenetic Signatures Associated with Growth and Shell Color in the Pacific Oyster, Crassostrea gigas

Fast growth is one of the most important breeding goals for all economic species such as the Pacific oyster (Crassostrea gigas), an aquaculture mollusk with top global production. Although the genetic basis and molecular mechanisms of growth-related traits have been widely investigated in the oyster, the role of DNA methylation involved in growth regulation remains largely unexplored. In this study, we performed a comparative DNA methylome analysis of two selectively bred C. gigas strains with contrasted phenotypes in growth and shell color based on whole-genome bisulfite sequencing (WGBS). Genome-wide profiling of DNA methylation at the single-base resolution revealed that DNA methylations were widely spread across the genome with obvious hotspots, coinciding with the distribution of genes and repetitive elements. Higher methylation levels were observed within genic regions compared with intergenic and promoter regions. Comparative analysis of DNA methylation allowed the identification of 339,604 differentially methylated CpG sites (DMCs) clustering in 27,600 differentially methylated regions (DMRs). Functional annotation analysis identified 11,033 genes from DMRs which were enriched in biological processes including cytoskeleton system, cell cycle, signal transduction, and protein biosynthesis. Integrative analysis of methylome and transcriptome profiles revealed a positive correlation between gene expression and DNA methylation within gene-body regions. Protein-protein interaction (PPI) analysis of differentially expressed and methylated genes allowed for the identification of integrin beta-6 (homolog of human ITGB3) as a hub modulator of the PI3K/Akt signaling pathway that was involved in various growth-related processes. This work provided insights into epigenetic regulation of growth in oysters and will be valuable resources for studying DNA methylation in invertebrates.

A single genomic region involving a putative chromosome rearrangement in flat oyster ( Ostrea edulis ) is associated with differential host resilience to the parasite Bonamia ostreae

European flat oyster (Ostrea edulis) is an ecologically and economically important marine bivalve, that has been severely affected by the intracellular parasite Bonamia ostreae. In this study, a flat oyster SNP array (~14,000 SNPs) was used to validate previously reported outlier loci for divergent selection associated with B. ostreae exposure in the Northeast Atlantic Area. A total of 134 wild and hatchery individuals from the North Sea, collected in naïve (NV) and long‐term affected (LTA) areas, were analysed. Genetic diversity and differentiation were related to the sampling origin (wild vs. hatchery) when using neutral markers, and to bonamiosis status (NV vs. LTA) when using outlier loci for divergent selection. Two genetic clusters appeared intermingled in all sampling locations when using outlier loci, and their frequency was associated with their bonamiosis status. When both clusters were compared, outlier data sets showed high genetic divergence (F_ST > 0.25) unlike neutral loci (F_ST not ≠ 0). Moreover, the cluster associated with LTA samples showed much higher genetic diversity and significant heterozygote excess with outlier loci, but not with neutral data. Most outliers mapped on chromosome 8 (OE‐C8) of the flat oyster genome, supporting a main genomic region underlying resilience to bonamiosis. Furthermore, differentially expressed genes previously reported between NV and LTA strains showed higher mapping density on OE‐C8. A range of relevant immune functions were specifically enriched among genes annotated on OE‐C8, providing hypotheses for resilience mechanisms to an intracellular parasite. The results suggest that marker‐assisted selection could be applied to breed resilient strains of O. edulis to bonamiosis, if lower parasite load and/or higher viability of the LTA genetic cluster following B. ostreae infection is demonstrated.