Marsupenaeus japonicus is an important marine crustacean species. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for genome-assisted breeding. Consequently, we determined the chromosome-level genome of M. japonicus. In total, 478.42 Gb of genomic sequencing data were obtained using the PacBio platform. A final genome assembly of 1.54 Gb was generated with a contig N50 of 229.97 kb. The 266 Contigs were categorized into 42 chromosomes using high‐throughput chromosome conformation capture (Hi-C) technology, with a scaffold N50 of 38.27 Mb, occupying 95.9% of the genome. We identified 24,317 protein-coding genes in the M. japonicus genome, among which annotation was available for 23,986 genes relying on information regarding known proteins in public databases. M. japonicus is commercially valuable because of its coloration and capability for live transport. A gene involved in heme oxygenase (decyclizing) activity and heme oxidation was identified under positive selection in M. japonicas. The truncated protein had an altered helical structure, which might be responsible for resistance to low oxygen, and even the colorful shell of M. japonicus. The high-quality genome assembly enabled the identification of genes associated with cold-stress and cold tolerance in kuruma shrimp through the comparison of eyestalk transcriptomes between the low temperature stressed shrimp and normal temperature shrimp. The genome assembly presented here could be useful in future studies to determine the genetic changes underpinning the ecological traits of M. japonicus, and provide insights for genome assisted breeding.

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1,465.32 Mb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.