Chromosome-level and high-contiguity genome assembly and annotation of the greasyback shrimp Metapenaeus ensis

The greasyback shrimp ( Metapenaeus ensis ) is an ecologically adaptable and economically important penaeid species. Here, we present its first chromosome-level genome assembly, generated by an integrated approach that combined Oxford Nanopore Technologies (ONT) long-read and Illumina short-read sequencing, followed by Hi-C scaffolding. The long-read data were pivotal for resolving a complex genomic architecture, featuring a genome-wide heterozygosity of 2.46% and a repetitive sequence content of 56.76%. The final assembly spans 1.97 Gb with a contig N50 of 3.84 Mb and a scaffold N50 of 45.37 Mb, 90.07% of the sequences were anchored onto 39 chromosomes. The assembly was annotated with 21,432 protein-coding genes. Assessment with BUSCO using the arthropoda_odb12 lineage dataset indicated high annotation completeness, with 95.6% of core arthropod genes identified as complete, including 89.1% as single-copy. This high-quality genomic resource provides a crucial foundation for advancing evolutionary, ecological, and aquaculture research on this species and related crustaceans.