Raw data from Litopenaeus vannamei genome sequencing and assembly

The Pacific white shrimp (Litopenaeus vannamei) is one of the most economically significant species in global aquaculture. We present a high-quality, chromosome-level genome assembly for L. vannamei, generated by integrating PacBio HiFi, Nanopore ultra-long, and Hi-C sequencing data. The final assembly spans 1.95 Gb (contig N50: 1.97 Mb), with approximately 97.25% of sequences anchored to 44 pseudochromosomes. Repetitive sequences constitute approximately 1.195 Gb, representing 61.28% of the genome. We annotated a total of 26,830 protein-coding genes, 23,952 of which were functionally characterized. The assembly exhibits exceptional completeness, achieving BUSCO scores of 70.98% (genome mode) and 69.8% (protein mode). This reference genome will serve as a fundamental resource for future genetic research on key economic traits and molecular breeding applications in L. vannamei.