Chromosome-level genome assembly of sea scallop Placopecten magellanicus provides insights into the genetic characteristics and adaptive evolution of large scallops.

Placopecten magellanicus (Gmelin, 1791), a deep-sea Atlantic scallop, holds significant commercial value as a benthic marine bivalve along the northwest Atlantic coast. Recognizing its economic importance, the need to reconstruct its genome assembly becomes apparent, fostering insights into natural resources and generic breeding potential. This study reports a high-quality chromosome-level genome of P. magellanicus, achieved through the integration of Illumina short read sequencing, PacBio HiFi sequencing, and Hi-C sequencing techniques. The resulting assembly spans 1778 Mb with a scaffold N50 of 86.71 Mb. An intriguing observation arises - the genome size of P. magellanicus surpasses that of its Pectinidae family peers by 1.80 to 2.46 times. Within this genome, 28,111 protein-coding genes were identified. Comparative genomic analysis involving five scallop species unveils the critical determinant of this expanded genome: the proliferation of repetitive sequences recently inserted, contributing to its enlarged size. The landscape of whole genome collinearity sheds light on the relationships among scallop species, enhancing our broader understanding of their genomic framework. This genome provides genomic resources for future molecular biology research on scallops and serves as a guide for the exploration of longevity-related genes in scallops.

Gray meat in the Atlantic sea scallop, Placopecten magellanicus, and the identification of a known pathogenic scallop apicomplexan.

Atlantic sea scallop (Placopecten magellanicus) meats are normally firm and creamy white. However, scallops with small, darkened and stringy adductor muscle (gray meat) episodically occur along the Eastern Seaboard, most recently in the rotational management areas of Georges Bank after extended fishing closures. These gray meat scallops are associated with reduced harvestable biomass and mass mortality events. We tested age, nutritional stress and disease as causative agents for this condition. Adult scallops of different shell heights (SH) ranging from (90-145mm) were collected from Georges Bank and analyzed for meat quality and the presence of pathogens using biochemical, histopathological and molecular methods. Gray meat occurrence was weakly correlated with shell height only explaining 8.49% of the variance in a generalized additive model (GAMS). Gray meat weights were lower than white meat (p<0.001) and there was a dramatic reduction in protein content (p<0.05) in gray meat scallops associated with extensive myodegeneration. Amino acid profiles confirmed the breakdown of muscle tissue with an increase in free hydroxyproline in gray meat scallops. Infection by an apicomplexan parasite was detected in the muscle tissue of all gray meat scallops tested. An intermediate pathology stage (brown meat) was also identified. As the parasitic infection increased, meat quality decreased. Numerous developmental stages of the parasite were present in various organs of the scallops. This apicomplexan has an identical SSU rDNA sequence to a novel parasite occurring in the Iceland scallop during a recent mass mortality event. The range of this parasite in Atlantic sea scallops and the effect of abiotic/biotic stressors on pathogenicity are currently unknown. Results from this study link an apicomplexan species, known to be highly pathogenic in scallops, to gray meat occurrence with a potentially high impact on the fishery.

Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus.

Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285-621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66-.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.

Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq-derived SNPs.

Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction-site-associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid-Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples, and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.