Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68 Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.

Takifugu species serve as a model system for evolutionary studies due to their compact genomes and diverse phenotypes. The ocellated puffer (Takifugu ocellatus), characterized by special colouration, is a scarce anadromous species in the genus Takifugu. As an ornamental and tasty fish species, T. ocellatus has moderate economic value. However, the available genomic resources for this pufferfish are still limited. Here, a chromosome-level reference genome, as well as two haploid genomes, was constructed by PacBio HiFi long sequencing and Hi-C technologies. The total length of the reference genome was 375.62 Mb with a contig N50 of 11.55 Mb. The assembled sequences were anchored to 22 chromosomes with an integration efficiency of 93.78%. Furthermore, 28,808 protein-coding genes were predicted. The haplotype-resolved reference genome of T. ocellatus provides a crucial resource for investigating the explosive speciation of the Takifugu genus, such as elucidating evolutionary histories, determining the genetic basis of trait evolution, and supporting future conservation efforts.

Larimichthys crocea is an endemic marine fish in East Asia that belongs to Sciaenidae in Perciformes. L. crocea has now been recognized as an "iconic" marine fish species in China because not only is it a popular food fish in China, it is a representative victim of overfishing and still provides high value fish products supported by the modern large-scale mariculture industry. Here, we report a chromosome-level reference genome of L. crocea generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The genome sequences were assembled into 1,591 contigs with a total length of 723.86 Mb and a contig N50 length of 2.83 Mb. After chromosome-level scaffolding, 24 scaffolds were constructed with a total length of 668.67 Mb (92.48% of the total length). Genome annotation identified 23,657 protein-coding genes and 7262 ncRNAs. This highly accurate, chromosome-level reference genome of L. crocea provides an essential genome resource to support the development of genome-scale selective breeding and restocking strategies of L. crocea.