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Mol Ecol Resour. 2019 Dec 30. doi: 10.1111/1755-0998.13132. [Epub ahead of print]

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

Kang S1, Kim JH1, Jo E1,2, Lee SJ2, Jung J1, Kim BM1, Lee JH1,3, Oh TJ4,5,6, Yum S7, Rhee JS8,9, Park H2.

Author information

1
Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon, Korea.
2
Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea.
3
Polar Sciences, University of Science & Technology, Daejeon, Korea.
4
Department of Life Science and Biochemical Engineering, SunMoon University, Asan, Korea.
5
Genome-based BioIT Convergence Institute, Asan, Korea.
6
Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Korea.
7
Risk Assessment Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje, Korea.
8
Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, Korea.
9
Research Institute of Basic Sciences, Incheon National University, Incheon, Korea.

Abstract

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.

KEYWORDS:

Takifugu obscurus ; Hi-C assembly; chromosome-level assembly; fugu genome; long-read sequencing

PMID:
31887246
DOI:
10.1111/1755-0998.13132

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