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.