Bivalve mollusks are economically important invertebrates that exhibit marked diversity in benthic lifestyle and provide valuable resources for understanding the molecular basis of adaptation to benthic life. In this report, we present a high-quality, chromosome-anchored reference genome of the Venus clam, Cyclina sinensis. The chromosome-level genome was assembled by Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 103 Genomics, and high-throughput chromosome conformation capture technologies. The final genome assembly of C. sinensis is 903.2 Mb in size, with a contig N50 size of 2.6 Mb and a scaffold N50 size of 46.5 Mb. Enrichment analyses of significantly expanded and positively selected genes suggested evolutionary adaptation of this clam to buried life. In addition, a change in shell color represents another mechanism of adaptation to burial in sediment. The high-quality genome generated in this work provides a valuable resource for investigating the molecular mechanisms of adaptation to buried lifestyle.

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BackgroundTo avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.ResultsThe clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.ConclusionsThe clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

Sexual differentiation and gonad development are important biological processes for bivalve species. The clam Cyclina sinensis is an important cultured marine bivalve widely distributed along with the coastal areas of China. However, the information related to sexual determination/differentiation and gonadal development of C. sinensis almost has no reported. To study the molecular mechanisms of its sexual determination/differentiation and gonadal development, transcriptome analysis was performed in the gonad of C. sinensis, and the potential biological functions of reproduction-related gene were also investigated in this study. The results showed that 1 013 and 427 genes were differentially expressed in the ovary and testis, respectively. KEGG enrichment analysis showed that the DEGs in the gonad were significantly clustered in progesterone-mediated oocyte maturation, cell cycle and oocyte meiosis. Further analysis showed that 23 genes were mainly involved in sex determination/differentiation, including Dmrt1, Sox2/4/9, Foxl2, β-catenin and GATA-type zinc finger protein 1-like. Twenty key genes were mainly involved in the process of spermatogenesis, and five genes encode steroid biosynthesis and metabolism. Fifteen genes related to ovarian development were also identified in this study, such as Vitellogenin, MAM and LDL-receptor class A domain-containing protein 1 and Cell division cycle protein 20 homolog. Moreover, 50µg/L estradiol treatment significantly up-regulated the expression levels of CsVg in the ovary and hepatopancreas. These results highlight the genes involved in sexual determination/differentiation and gonadal development, which enhance our understanding for further studies of reproduction and breeding of C. sinensis and other marine bivalves.

The clam Cyclina sinensis is one of the important economical aquaculture shellfish in China. However, the mechanisms of sex determination and differentiation in C. sinensis have not been fully studied. In this study, full-length cDNAs of DMRT3 and FOXL2 were cloned and functionally characterized. The ORF region of CsDMRT3 consists of 1137 nucleotides, which encode 378 amino acids contains a conserved DM domain of DMRT family. The ORF region of CsFOXL2 is 1245 bp, encodes 414 amino acids, and contains a conserved FH domain. Tissue-specific expression results showed that the higher expression level of CsDMRT3 and CsFOXL2 was found in the ovary and testis of C. sinensis. The expression levels of CsDMRT3 and CsFOXL2 also peaked at the maturation stage of male and female gonadal development, respectively. Moreover, the expression levels of CsDMRT3 and CsFOXL2 were significantly higher in the trochophore and D-larval stages than in other stages. The transcript levels of CsDMRT3 reached the highest level at 11 months of age, while the CsFOXL2 reached the highest level at 7 months of age. In estradiol-treated experiments, the expression levels of CsDMRT3 and CsFOXL2 in the gonads were highest at 5 µg/L estradiol treatment, and histologically, it was observed that the oocytes diameters became larger with increasing estradiol concentration. These results suggest that CsDMRT3 and CsFOXL2 play an important role in gonadal development and sex differentiation of C. sinensis.