Chromosome-level haplotype-resolved genome assembly for Takifugu ocellatus using PacBio and Hi-C technologies.

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.

Zeng Q ，Zhou Z ，He Q ，Li L ，Pu F ，Yan M ，Xu P ... -  《Scientific Data》

Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis.

The Tetraodontidae family are known to have relatively small and compact genomes compared to other vertebrates. The obscure puffer fish Takifugu obscurus is an anadromous species that migrates to freshwater from the sea for spawning. Thus the euryhaline characteristics of T. obscurus have been investigated to gain understanding of their survival ability, osmoregulation, and other homeostatic mechanisms in both freshwater and seawater. In this study, a high quality chromosome-level reference genome for T. obscurus was constructed using long-read Pacific Biosciences (PacBio) Sequel sequencing and a Hi-C-based chromatin contact map platform. The final genome assembly of T. obscurus is 381 Mb, with a contig N50 length of 3,296 kb and longest length of 10.7 Mb, from a total of 62 Gb of raw reads generated using single-molecule real-time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome-scale scaffolds using a Hi-C approach, resulting in a 373 Mb genome assembly with a contig N50 length of 15.2 Mb and and longest length of 28 Mb. When we directly compared the 22 longest scaffolds of T. obscurus to the 22 chromosomes of the tiger puffer Takifugu rubripes, a clear one-to-one orthologous relationship was observed between the two species, supporting the chromosome-level assembly of T. obscurus. This genome assembly can serve as a valuable genetic resource for exploring fugu-specific compact genome characteristics, and will provide essential genomic information for understanding molecular adaptations to salinity fluctuations and the evolution of osmoregulatory mechanisms.

Kang S ，Kim JH ，Jo E ，Lee SJ ，Jung J ，Kim BM ，Lee JH ，Oh TJ ，Yum S ，Rhee JS ，Park H ... -  《-》

The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies.

Zhou Z ，Liu B ，Chen B ，Shi Y ，Pu F ，Bai H ，Li L ，Xu P ... -  《Scientific Data》

Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata).

Liu D ，Tian X ，Shao S ，Ma Y ，Zhang R ... -  《Scientific Data》

Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data.

Zhou Y ，Xiao S ，Lin G ，Chen D ，Cen W ，Xue T ，Liu Z ，Zhong J ，Chen Y ，Xiao Y ，Chen J ，Guo Y ，Chen Y ，Zhang Y ，Hu X ，Huang Z ... -  《Scientific Data》