Chromosome-level genome assembly of the bay scallop Argopecten irradians

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.

海湾扇贝（*Argopecten irradians*）是兼具重要商业、文化与生态价值的物种。该物种原产于美国东海岸，后被引入中国，支撑了中国规模可观的扇贝水产养殖业。本研究构建了基于PacBio与Hi-C技术组装的海湾扇贝注释版染色体水平参考基因组。该基因组总长度为845.9 Mb，共包含1503个scaffold（支架序列），其scaffold N50值为44.3 Mb。组装完成的基因组中，92.9%的序列集中于16个最大的支架序列，对应经Hi-C分析验证的16条染色体。本次组装还涵盖了完整的线粒体基因组。该基因组约36.2%的序列为重复元件。BUSCO（Benchmarking Universal Single-Copy Orthologs）分析显示该基因组组装的完整度为96.2%。本研究共注释得到33772个蛋白质编码基因。该基因组组装将为后续的进化动力学、适应机制研究提供宝贵资源，同时将支持基因组辅助育种工作，有助于在面临环境与病原挑战时，对这一标志性物种开展保护与管理。