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Chromosomal­level assembly of Takifugu obscurus (Abe, 1949) genome using third­generation DNA sequencing and Hi­C analysis

Cited 3 time in wos
Cited 3 time in scopus
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Title
Chromosomal­level assembly of Takifugu obscurus (Abe, 1949) genome using third­generation DNA sequencing and Hi­C analysis
Other Titles
3세대 DNA 시퀀싱과 Hi-C를 이용한 황복의 염색체 수준의 유전체 분석
Authors
Kang, Seunghyun
Kim, Jin-Hyoung
Jo, Euna
Lee, Seung Jae
Jeong, Jihye
Kim, Bo-Mi
Lee, Jun Hyuck
Oh, Tae-Jin
Yum, Seungshic
Rhee, Jae-Sung
Park, Hyun
Subject
Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology
Keywords
chromosome-level assembly; fugu genome; Hi-C assembly; long-read sequencing; Takifugu obscurus
Issue Date
2020-03
Citation
Seunghyun Kang, et al. 2020. "Chromosomal­level assembly of Takifugu obscurus (Abe, 1949) genome using third­generation DNA sequencing and Hi­C analysis". MOLECULAR ECOLOGY RESOURCES, 20(2): 520-530.
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 Hi­C­based 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 single­molecule real­time sequencing technology from a PacBio Sequel platform. The PacBio data were further clustered into chromosome-scale scaffolds using a Hi­C 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
URI
https://repository.kopri.re.kr/handle/201206/11768
DOI
http://dx.doi.org/10.1111/1755-0998.13132
Appears in Collections  
2018-2019, Genome Analysis of Marine Animals (18-19) / Park, Hyun (PM18080)
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