Chromosome-level genome assembly of the bay scallop Argopecten irradians

Abstract

The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

Fig. 1

A representation of color and pattern variations in Argopecten irradians, commonly known as the bay scallop. Photo: S. Tettelbach.

Fig. 2

Chromosomal organization and synteny in Argopecten irradians NY. (a) A circular genomic map illustrating 16 chromosomes with color-coded segments (I), detailing GC content (II), gene (III) and repeated sequence density (IV). Interconnecting lines (V) represent syntenic blocks and conserved genomic regions across the chromosomes. (b) Contact map of the A. irradians genome assembly. Map generated from Hi-C data showing sequence interaction points in chromosomes (red dots). The color bar indicates contact density. (c) Genomic collinearity between A. irradians and the king scallop, P. maximus.

Fig. 3

Gene family dynamics and functional enrichment in molluscan evolution. (a) Phylogenetic analysis and gene family evolution of 11 molluscan species. Tree topology with estimated divergence times (million years ago, MYA, including range) is shown next to each lineage (blue). Number of expanded (green) and contracted (red) gene families shown next each branch. The right panel illustrates the distribution of gene families among 11 molluscan species. It shows the number of shared single-copy genes (red), which are present in all analyzed genomes but exist in only one copy per individual genome; shared multiple-copy genes (yellow), which are present in all analyzed genomes and exist in multiple copies in individual genomes; genes found only in Argopecten species (green); genes found in Pectinidae species (purple); genes found only in the corresponding species (blue); and other species-combination of orthologous genes (grey). (b) Venn Diagram graph of orthologous gene families shared/not shared among 11 molluscan species. (c) Enriched KEGG pathway analysis for expanded gene families in Argopecten irradians. The bubble plot illustrates the top 20 enriched pathways, where the bubble size reflects the number of genes and the color gradient (-log₁₀(P-value)) indicates the significance of the enrichment.