The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae. A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated. We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.

Salinity can affect the physiological and productive characteristics of bivalves. The razor clam Sinonovacula constricta naturally distributing in intertidal zones and estuarine waters is extensively cultured in China. High-salinity is a serious threat to its culture, especially in pond culture model. Here, we investigated the effects of high-salinity on the survival, gill tissue, enzyme activity and free amino acid content of S. constricta. Individuals were randomly divided into six groups treated with different salinities of 20, 25, 30, 35, 40, and 45 ppt. The median lethal salinity calculated by linear regression and probit analysis methods were similar, with 46.61, 43.17, 36.99, 35.99, and 34.99 ppt by linear regression, while 44.63, 42.87, 38.45, 37.32, and 36.17 ppt by probit analysis at 72, 96, 120, 144, and 168 h, respectively. Furthermore, paraffin section revealed that the gill of razor clam shrunk quickly under high-salinity and dissolved at 48 h under salinity of 40 ppt, but not under 30 ppt. In addition, the activities of three enzymes including Na⁺-K⁺-ATPase, acid phosphatase and alkaline phosphatase changed significantly under high-salinity. Besides, the contents of total free amino acids (TFAAs) in the gill tissues were 61.25 ± 1.58, 89.36 ± 4.18, and 111.98 ± 1.46 mg⋅g^–1 at salinity of 20, 30, and 40 ppt, respectively, indicating increasing TFAA contents with salinity. Notably, several amino acid species including taurine, alanine, proline, glycine and glutamic showed significantly changed contents in response to salinity variation, suggesting these amino acids might play an important role in razor clam’s adaptation to salinity stress. Combining all these results, it was referred that razor clams may adapt to moderately high-salinity of 30 ppt in a short time through osmotic adjustment. Although a small proportion of individuals could survive under the salinity of 35 ppt, the death of most individuals still suggested it can hardly be accepted in aquacultural production. Notably, living under a salinity of 40 ppt for more than 48 h could cause great damage to razor clams. Therefore, the seawater salinity is recommended to be lower than 30 ppt for S. constricta aquaculture. Overall, this study provides guidance for the culture and breeding of high-salinity tolerant razor clams.

Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis. Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle. For the same comparison, iTRAQ-based proteomics reveals 474 differentially expressed proteins (DEPs), 198 up- and 276 downregulated. These DEPs mainly comprise muscle-specific proteins of the sarcoplasmic reticulum, extracellular matrix, and metabolic pathways. A group of conventional muscle proteins—myosin heavy chain, myosin regulatory light chain, myosin essential light chain, and troponin—are enriched in fast muscle. In contrast, paramyosin, twitchin, and catchin are preferentially expressed in slow muscle. The association analysis of proteomic and transcriptomic data provides the evidences of regulatory events at the transcriptional and posttranscriptional levels in fast and slow muscles. Among 1236 differentially expressed unigenes, 22.7% show a similar regulation of mRNA levels and protein abundances. In contrast, more unigenes (53.2%) exhibit striking differences between gene expression and protein abundances in the two muscles, which indicates the existence of fiber-type specific, posttranscriptional regulatory events in most of myofibrillar proteins, such as myosin heavy chain, titin, troponin, and twitchin. This first, global view of protein and mRNA expression levels in scallop fast and slow muscles reveal that regulatory mechanisms at the transcriptional and posttranscriptional levels are essential in the maintenance of muscle structure and function. The existence of fiber-type specific, posttranscriptional regulatory mechanisms in myofibrillar proteins will greatly improve our understanding of the molecular basis of muscle contraction and its regulation in non-model invertebrates.

The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N_e). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H_o) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H_e) was calculated to be varying from 0.587 to 0.700. F_st values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F_st values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean F_ST of the total population was 0.4534). Pairwise F_ST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.