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.

中文翻译：

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使用第三代DNA测序和Hi-C分析，对暗色T草（Takifugu obscurus）（Abe，1949）基因组进行染色体水平装配。

与其他脊椎动物相比，已知四齿科具有相对较小和紧凑的基因组。河豚T鱼（Takifugu obscurus）是一种无孔鱼类，它从海中迁移到淡水以产卵。因此，已经研究了暗线虫的淡碱性特征，以了解它们在淡水和海水中的存活能力，渗透调节作用和其他稳态机制。在这项研究中，使用长期阅读的太平洋生物科学公司（PacBio）的Sequel测序和基于Hi-C的染色质接触图平台，构建了暗线虫的高质量染色体水平参考基因组。T. obscurus的最终基因组组装为381 Mb，重叠群N50长度为3,296 kb，最长长度为10.7 Mb，从PacBio Sequel平台使用单分子实时测序技术产生的总计62 Gb的原始读数中提取。使用Hi-C方法将PacBio数据进一步聚类到染色体规模的支架中，从而得到373 Mb基因组装配体，其重叠群N50长度为15.2 Mb，最长长度为28 Mb。当我们直接比较暗藏红豆杉的22个最长的支架与老虎河豚T（Takifugu rubripes）的22条染色体时，在这两个物种之间观察到了清晰的一对一直系同源关系，这支持了暗藏红豆杉的染色体水平装配。这种基因组组装可以作为探索河豚特有的紧凑型基因组特征的宝贵遗传资源，