Charybdis japonica predominantly inhabits the intertidal zones and has high desiccation tolerance. We present the first chromosome-level C. japonica genome, which contains 51 chromosomes, and the revised genome is 1431.02 Mb in length and has a contig N50 size of 29.67 Mb. Among the contigs, 91.42% were anchored to 51 chromosomes. Additionally, 824.02 Mb repeat elements, 30,900 coding genes, 474 miRNAs, 15,570 tRNAs, 309 rRNAs, and 157 miRNAs were identified in the C. japonica genome. The whole-genome resequencing data can contribute to the identification of sex-related single-nucleotide polymorphisms and insertion–deletion mutations. The 0-10,120,000 bp of chromosome 37 is the sex-determining region of C. japonica. Comparative genome analysis identified 1,138 C. japonica-specific gene families. Phylogenetic analysis showed that C. japonica has a close relationship with Portunus trituberculatus, which also belonged to family Portunidae, and differentiated 42.1-135.5 million years ago. Demographic history analysis suggested that the maximum effective population size of C. japonica was maintained until 0.5×105 years ago. Relative evolution rate showed that C. japonica evolved slower than Daphnia magna, Penaeus vannamei, and P. trituberculatus. Compared with other species, metabolism rate, oxygen supply, oxidative stress, and various transporter-related genes were expanded or underwent positive selection in C. japonica, which might contribute to C. japonica’s ability to overcome diverse stresses in drought environment. Decoding the present genome provides valuable information for revealing the desiccation-adaptive and sex-determining mechanisms of C. japonica and also enriches the genetic information to explore the evolutionary history and environmental adaptation strategies of other Portunidae crabs.

Acanthogobius ommaturus is a large, economically important annual fish widely distributed in coastal and estuarine areas. The adults will die after breeding, and its life cycle is only one year. The first chromosome-level genome assembly of A. ommaturus was obtained by PacBio and Hi-C sequencing in this study. The final genome assembly after Hi-C correction was 921.49 Mb, with contig N50 and scaffold N50 values of 15.70 Mb and 40.99 Mb, respectively. The assembled sequences were anchored to 22 chromosomes by using Hi-C data. A total of 18,752 protein-coding genes were predicted, 97.90% of which were successfully annotated. A. ommaturus is phylogenetically closely related to Periophthalmodon magnuspinnatus, Boleophthalmus pectinirostris, diverging approximately 31.9 million years ago with the two goby species. The A. ommaturus genome displayed 597 expanded and 3,094 contracted gene families compared with the common ancestor. A total of 1155 positive selected genes (PSGs) (p < 0.05) were identified. Based on comparative genomic analyses, we obtained several expanded genes such as ACSBG2, LRP1, LRP6 and ZNF638 involved in lipid metabolism. Totally twenty candidate genes were identified under positive selection, which associated with lifespan including ERCC6, IGF1, POLG, and TERT. Interspecific collinearity analysis showed a high genomic synteny between A. ommaturus and Periophthalmodon magnuspinnatus. The effective population size of A. ommaturus decreased drastically during 200-100Ka because of Guxiang ice age, then increased gradually following warm periods. This study provides pivotal genetic resources for in-depth biological and evolutionary studies, and underlies the molecular basis for lipid metabolism.

Knowledge about the genetic adaptations of various organisms to heterogeneous environments in the Northwestern Pacific remains poorly understood. The mechanism by which organisms adapt to temperature in response to climate change must be determined. We sequenced the whole genomes of Sillago japonica individuals collected from different latitudinal locations along the coastal waters of China and Japan to detect the possible thermal adaptations. A total of 5.48 million single nucleotide polymorphisms (SNPs) from five populations revealed a complete genetic break between the China and Japan groups. This genetic structure was partly attributed to geographic distance and local adaptation. Although parallel evolution within species is comparatively rare at the DNA level, the shared natural selection genes between two isolated populations (Zhoushan and Ise Bay/Tokyo Bay) indicated possible parallel evolution at the genetic level induced by temperature. Our result proved that the process of temperature selection on isolated populations is repeatable. Additionally, the candidate genes were functionally related to membrane fluidity in cold environments and the cytoskeleton in high-temperature environments. These results advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish species. Projections of species distribution models suggested that China and Japan groups may have different responses to future climate changes: the former could expand, whereas the latter may contract. The results of the present population genomic work expand our understanding of genetic differentiation and adaptation to changing environments.

The burbot (Lota lota) is the only member of the cod family (Gadidae) that is adapted solely to freshwater. This species shows the widest longitudinal range of freshwater fish in the world. The burbot is a good model for studies on adaptive genome evolution from marine to freshwater environment. However, no high-quality reference genome has been released. Here, the first chromosome-level genome of the burbot was constructed using PacBio long sequencing and Hi-C technology. A total of 95.24 Gb polished PacBio sequences were generated, and the preliminary genome assembly was 575.83 Mb in size with a contig N50 size of 2.15 Mb. The assembled sequences were anchored to 22 pseudo-chromosomes by using the Hi-C data. The final assembled genome after Hi-C correction was 575.92 Mb, with a contig N50 of 2.01 Mb and a scaffold N50 of 22.10 Mb. A total of 22,067 protein-coding genes were predicted, 94.82% of which were functionally annotated. Phylogenetic analyses indicated that burbot diverged with the Atlantic cod about 44.4 million years ago. In addition, 377 putative genes that appear to be under positive selection in burbot were identified. These positively selected genes might adapt to the freshwater environment. These genome data provide an invaluable resource for the ecological and evolutionary study of the order Gadiformes.