Genome assembly and annotation files of sea scallop Placopecten magellanicus

<em>Placopecten magellanicus</em> (Gmelin), a deep-sea Atlantic scallop naturally found along the northwest Atlantic coast, is a commercially essential benthic large marine bivalve. Given the commercial importance of sea scallop <em>P. magellanicus</em>, it is necessary to reconstruct its genome to benefit the further exploration of natural resources, even genetic breeding. Herein, we first reported a high-quality chromosome-level genome of sea scallop <em>P. magellanicus</em> using a combination of Illumina short read sequencing, PacBio HiFi reads, and Hi-C sequencing. Our approach allowed us to obtain a final assembly comprising 1,778 Mb of sequence and a N50 scaffold of 86.71 Mb.