The Pacific oyster, Crassostrea gigas, belongs to one of the most species-rich phyla and provides important ecological and economical services. Here we present a genome assembly for a variety of this species, black-shelled Pacific oyster, using a combination of 61.8 Gb Nanopore long reads and 105.6 Gb raw BGI-seq short reads. The genome assembly comprised 3,676 contigs, with a total length of 587 Mb and a contig N50 of 581 kb. Annotation of the genome assembly identified 283 Mb (48.32%) of repetitive sequences and a total of 26,811 protein-coding genes. A long-term transposable element active, accompanied by recent expansion (1 million years ago), was detected in this genome. The divergence between black-shelled and the previous published Pacific oysters was estimated at about 2.2 million years ago, which implies that species C. gigas had great intraspecific genetic variations. Moreover, we identified 148/188 specifically expanded/contracted gene families in this genome. We believe this genome assembly will be a valuable resource for understanding the genetic breeding, conservation, and evolution of oysters and bivalves.

The Pacific oyster, Crassostrea gigas, is widely distributed and is substantially important to shellfish cultivation. Oysters with melanin-colored shells and soft parts are increasingly popular and are of high economic value. However, the distribution and synthesis of melanin in C. gigas remains unclear and there have been only few relevant studies on it. In this study, transmission electron microscopy (TEM) was used to observe melanin in the epidermis of dark mantle tissue. Melanocytes containing melanosomes were observed below the epidermis, suggesting the possibility of a gradual transfer of melanin from the mantle tissue to the epithelium. The frozen section technique and three melanin staining methods were used to confirm the presence of melanin. The results suggest that enzyme identification (DOPA) is a suitable method of melanin staining in the mantle tissues of C. gigas. This study preliminarily identified the existence of melanin in the mantle tissues of C. gigas and is a foundation for the study of melanin synthesis. Furthermore, it provides new insights into the mechanism of shell color formation.

Background: Growth hormone inducible transmembrane protein (GHITM) is a highly conserved transmembrane protein. This study was conducted to investigate the role of GHITM gene in the apoptosis and growth of the golden apple snail Pomacea canaliculate.Results: The complete cDNA of this gene was cloned using the rapid amplification of cDNA ends (RACE) method and subjected to bioinformatics analysis. The full-length cDNA was 2242 bp, including an open reading frame of 1021 bp that encoded a protein of 342 amino acid residues. The mRNA expression profiles of GHITM gene in different tissues (liver, kidney, gonad and foot) and different growth phases (6-months old and 2-years old) showed that it was expressed in various tissues and different growth phases. Silencing of the GHITM gene by RNAi (RNA interference) experiments revealed that the GHITM gene possibly plays a role in inhibiting apoptosis through detecting the Caspase (Cysteine-requiring Aspartate Protease)-3 activity. In addition, the aperture width and body whorl length of the snail was significantly affected by RNAi, suggesting that this gene plays a significant role in promoting the growth of the organism. Conclusions:These results demonstrated that the GHITM gene was involved in apoptosis and growth in golden apple snail.

The DNA in the shell of Crassostrea gigas could have important roles in the shell biomineralization. However, limited by the low efficiency of existing extraction methods, studies investigating the DNA in shells are lacking. In this study, the shell DNA of C. gigas was extracted using the organic solvent extraction (OSE) and guanidine lysis buffer (GLB) methods; the efficiency and quality of these two methods were compared. The sequences of a mitochondrial gene (cytochrome c oxidase subunit I, COI) and a nuclear gene (28S rRNA) of C. gigas were analyzed to verify the origin of the extracted shell DNA. Finally, the DNA contents of the ventral edge, middle part, and dorsal edge of C. gigas shells were compared. The results showed that OSE had a higher DNA extraction efficiency than GLB; the oyster shell DNA was homologous to the oyster genome; the DNA content was higher in the ventral edge than in the middle part or in the dorsal edge of the C. gigas shell. This study not only reports an improved extraction method for the mollusk shell DNA, but also revealed that the DNA in the oyster shell originates from the oyster body and that the DNA content in different parts of the C. gigas shell showed obvious variance. These results provide supporting evidence for the hypothesis that oyster cells participate in shell formation, and also afford a nondestructive method for oyster genetic identification, which can promote the application of molecular biology technology in oyster breeding. In addition, a shell growth pattern of ‘Under Old & Exceeding Old’ was also proposed.

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