Chromosome-level genome assembly and annotation of the kuruma shrimp Marsupenaeus japonicus

The kuruma shrimp Marsupenaeus japonicus is one of the most economically important shrimp species in the world. Here, we constructed a chromosome-level genome assembly of M. japonicus by combining PacBio long reads, Illumina short reads and Hi-C scaffolding. The genome size was 1.64 Gb with a scaffold N50 length of 40.61 Mb, and 97.83% (1.60 Gb) of the assembled sequences were anchored to 43 chromosomes. The genome contained 62.79% repeat sequences and 21,172 protein-coding genes, of which 83.20% were functionally annotated. The completeness of M. japonicus genome assembly is highlighted by a BUSCO score of 91.0%. Evolutionary analysis indicated that M. japonicus was closely related to Litopenaeus vannamei and Penaeus monodon, with an estimated divergence time from their common ancestor of 88.33 million years ago. In sum, the chromosome-level genome assembly and annotation provide fundamental resources for genetic breeding and molecular mechanism related studies of M. japonicus.