Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.

Shell characterization and effects on cavity volume of wild Jinjiang oyster Crassostrea ariakensis in different estuaries of China

Jinjiang oyster Crassostrea ariakensis,a species with economic and ecological value,is distributed along the estuaries and coasts of East Asia.With the decline in natural resources,the conservation and aquaculture of this species is urgent.However,studies characterizing their shell shape remain scarce.We investigated the morphological differences in the shells of wild Jinjiang oysters from six populations(Qinzhou,Shanghai,Nantong,Qingdao,and Binzhou hard or muddy bottom)along the coast of China.The color of the shell and adductor muscle scar showed associations with temperature gradient along its geographical distribution.Oyster shape was defined by shell height to shell length ratio,and the ratio varies among geographic locations of the populations.They were found nearly round(Qinzhou and Nantong populations),oval(Qingdao and Binzhou populations),or water-droplet-shaped(Shanghai population).Binzhou populations living on muddy substrates are more elongated than those on hard substrate.In addition,we developed a method to measure the cavity volume in oysters.Correlation and path analysis showed that shell height significantly influenced cavity volume.The synergistic effect of the two factors(the height,length,and width of the shell in pairs)on the cavity volume resulted in differences between northern and southern groups:samples from the southern group(Qinzhou and Shanghai)showed correlation between shell height and shell width,while those from the northern group(Nantong,Qingdao,and Binzhou)showed correlation between shell height and shell length.All populations showed significant correlation between shell height and cavity height,and shell length and cavity length,while the correlation between shell width and cavity width was minimal,which may have been resulted from uneven shell thickness.The linear equation for shell height and cavity volume under different ratios of shell height to length was obtained.In this study,we determined that shell height has the most influence on cavity volume,and specific cavity volume fitting linear equations are given for different shell types,which may provide a reference for future oyster breeding for shell shaping.

Combined effects of temperature and copper ion concentration on the superoxide dismutase activity in Crassostrea ariakensis

Superoxide dismutase（SOD） is a crucial antioxidant enzyme playing the first defense line in antioxidant pathways against reactive oxygen species in various organisms including marine invertebrates. There exist mainly two specific forms, Cu/Zn-SOD（SOD1） and Mn-SOD（SOD2）, in eukaryotes. SODs are known to be concurrently modulated by a variety of environmental stressors. By using central composite experimental design and response surface method, the joint effects of water temperature（18–34°C） and copper ion concentration（0.1–1.5 mg/L） on the total SOD activity in the digestive gland of Crassostrea ariakensis were studied. The results showed that the linear effect of temperature was highly significant（P〈0.01）, the quadratic effect of temperature was significant（P〈0.05）; the linear effect of copper ion concentration was not significant（P〉0.05）, while the quadratic effect of copper ion concentration was highly significant（P〈0.01）; the interactive effect of temperature and copper ion concentration was not significant（P〉0.05）; the effect of temperature was greater than that of copper ion concentration. The model equation of digestive gland SOD enzyme activity towards the two factors of interest was established, with R2 and predictive R2 as high as 0.961 6 and 0.820 7, respectively, suggesting that the goodness-offit to experimental data be very satisfactory, and could be applied to prediction of digestive gland SOD activity in C. ariakensis under the conditions of the experiment. Our results would be conducive to addressing the health of aquatic animals and/or to detecting environmental problems by taking SOD as a potential bioindicator.