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

Cited 7 time in WEB OF SCIENCE
Title
Chromosomal-level assembly of Takifugu obscurus (Abe, 1949) genome using third-generation DNA sequencing and Hi-C analysis
Author(s)
Kang, Seunghyun; Kim, Jin-Hyoung; Jo, Euna; Lee, Seung Jae; Jung, Jihye; Kim, Bo-Mi; Lee, Jun Hyuck; Oh, Tae-Jin; Yum, Seungshic; Rhee, Jae-Sung; Park, Hyun
KIOST Author(s)
Yum, Seung Shic(염승식)
Publication Year
2020-03
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.
ISSN
1755-098X
URI
https://sciwatch.kiost.ac.kr/handle/2020.kiost/405
DOI
10.1111/1755-0998.13132
Bibliographic Citation
MOLECULAR ECOLOGY RESOURCES, v.20, no.2, pp.520 - 530, 2020
Publisher
WILEY
Subject
DE-NOVO IDENTIFICATION; RED-BLOOD-CELLS; TRANSPOSABLE ELEMENTS; PHYLOGENETIC ANALYSIS; TELEOST FISH; CLASS-I; FUGU; ANNOTATION; EVOLUTION; POTASSIUM
Keywords
chromosome-level assembly; fugu genome; Hi-C assembly; long-read sequencing; Takifugu obscurus
Type
Article
Language
English
Document Type
Article
Publisher
WILEY
Files in This Item:
There are no files associated with this item.

qrcode

Items in ScienceWatch@KIOST are protected by copyright, with all rights reserved, unless otherwise indicated.