The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.

The two subspecies of Atlantic bay scallop (Argopecten irradians), A. i. irradians and A. i. concentricus, are economically important aquacultural species in northern and southern China. Here, we performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for A. i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7 Mb and 874.82 Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54 kb and 1.53 Mb for the A. i. irradians genome, and those for the A. i. concentricus genome were 63.73 kb and 1.25 Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for A. i. irradians and A. i. concentricus, respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding.

Color polymorphism, a high-valued trait, is frequently observed in molluscan shellfish. The QN Orange scallop, a new scallop strain successively selected from the interspecific hybrids of the bay scallop (Argopecten irradians irradians) and the Peruvian scallop (Argopecten purpuratus), is distinguished from other scallops by its orange adductor muscles. In this study, to reveal the mechanisms of the formation of adductor muscle coloration in the QN Orange scallops, we compared the proteome and transcriptome of orange adductor muscles of the QN Orange and those of white adductor muscles of the Bohai Red scallop, another strain selected from the interspecific hybrids of the bay scallop and the Peruvian scallop. Transcriptomic analysis revealed 416 differentially expressed genes (DEGs) between white and orange adductor muscles, among which 216 were upregulated and 200 were downregulated. Seventy-four differentially expressed proteins (DEPs), including 36 upregulated and 38 downregulated proteins, were identified through label-free proteomics. Among the identified DEGs and DEPs, genes related to carotenoids biosynthesis including apolipophorin, and Cytochrome P450 and those related to melanin biosynthesis including tyrosinase and Ras-related protein Rab-11A were found to express at higher levels in orange adductor muscles. The high expression levels of VPS (vacuolar protein sorting) and TIF (translation initiation factor) in orange adductor muscle tissues indicated that carotenoid accumulation may be affected by proteins outside of the carotenoid pathway. Our results implied that the coloration of orange adductor muscles in the QN Orange scallops may be controlled by genes modulating accumulation of carotenoids and melanins. This study may provide valuable information for understanding the mechanisms and pathways underlying adductor muscle coloration in molluscan shellfish.

Ark shells (Scapharca subcrenata) grown on the tidal flats are often exposed to high temperature stresses in summer. In order to better understand their adaption to extreme or natural high temperature, we first determined the 96-h upper lethal temperature of ark shell and then investigated their physiological and transcriptional responses to acute or chronic thermal stress at the 96-h upper median lethal temperature (32°C). A significantly higher cumulative mortality (52% in 96 h) was observed in the acute heating treatment (AHT) group than that (22% in 7 days) in the chronic heating treatment (CHT) group. The apoptosis and necrosis rates of hemocytes were increased significantly in a time-dependent manner under both thermal stress strategies. Activities of antioxidant enzymes [superoxide dismutase (SOD) and catalase (CAT)] increased dramatically in a short time followed by a quick decline and reached to a lower level within 12 h in the AHT group, but maintain relatively high levels over a long period in the CHT group. The contents of malondialdehyde (MDA) were increased significantly firstly and restored to the original later in both acute and chronic thermal stress. Moreover, expression of the genes related to heat shock proteins (HSPs; HSP90, HSP70, HSP20, and sHSP), apoptosis [TNF receptor-associated factor 6 (TRAF6), glucose regulated protein 78 kD (GRP78), and caspase-3 (Casp-3)] and antioxidant responses [glutathione S-transferase (GST) and multidrug resistance protein (MRP)] could be induced and up-regulated significantly by thermal stress, however, expression of regucalcin (RGN), metallothionein (MT), and peroxiredoxin (PRX) was down-regulated dramatically under the two heating treatments. These results suggested that anti-apoptotic system, antioxidant defense system and HSPs could play important roles in thermal tolerance of ark shells, and the heat-resistant ark shell strains could be selected continuously by properly chronic thermal stress.