A high-quality genome assembly of the Pacific white shrimp (Litopenaeus vannamei) provides insights into its evolution and adaptation

Abstract

The Pacific white shrimp (Litopenaeus vannamei) is the most commercially-farmed shrimp species globally and is of significant ecological and economic importance. Here we report a high-quality genome assembly of L. vannamei using PacBio reads and Hi-C data. The assembly spans 1.87 Gb with scaffold N50 of 39.7 Mb and 87% of estimated genome size is assigned to 44 pseudochromosomes. The genome contains 24,861 protein-coding genes and a high proportion of transposable elements (64.33%). Significant expansion of gene families was observed in the genome related to locomotion, vision, and neural transmission, including via expansion of actin, myosin, rhodopsin, and neurotransmitter-gated ion-channel ligand binding domain genes, potentially revealing mechanisms underlying their evolved benthic adaptations. The genome assembly of L. vannamei provides valuable resources for future genetic research, breeding, and improvement of aquaculture traits, and will facilitate the research of genetic changes during evolution.