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.

The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis, L. polyactis) an appealing model for studying the formation of hermaphrodites. On the other hand, as the most famous commercial fish species in East Asia, the origin and evolutionary relationship of L. polyactis and Larimichthys crocea remain unclear. Here, we report the genome sequence of L. polyactis, with a size of ~706 Mb (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and 25,233 protein-coding genes. Phylogenomic analysis suggests that L. polyactis diverged from the common ancestor of Larimichthys crocea ~25.4 million years ago. Our high-quality genome assembly enabled comparative genomic analysis, which revealed a number of within-chromosome rearrangements and translocations without major chromosome fission or fusion events between the two species. The dmrt1 gene was identified as the candidate sex determination gene in L. polyactis. The expression of dmrt1 and its upstream regulatory gene rnf183 were both sexually dimorphic in the transcriptome analysis. Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in Larimichthys but not in other teleost species, suggesting that it originated from a lineage-specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in male L. polyactis may be explained by the sequence evolution of dmrt1. Decoding the L. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution but also provides valuable information for enhancing fish aquaculture.