IOCAS-IR
Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae
Xiao, Yongshuang1,2,3; Xiao, Zhizhong1,2,3; Ma, Daoyuan1,2,3; Liu, Jing1,2,3; Li, Jun1,2,3
2019-03-01
Source PublicationGIGASCIENCE
ISSN2047-217X
Volume8Issue:3Pages:8
Corresponding AuthorLiu, Jing(jliu@qdio.ac.cn) ; Li, Jun(junli@qdio.ac.cn)
AbstractBackground: The barred knifejaw (Oplegnathus fasciatus), a member of the Oplegnathidae family of the Centrarchiformes, is a commercially important rocky reef fish native to East Asia. Oplegnathus fasciatus has become an important fishery resource for offshore cage aquaculture and fish stocking of marine ranching in China, Japan, and Korea. Recently, sexual dimorphism in growth with neo-sex chromosome and widespread biotic diseases in O. fasciatus have been increasing concern in the industry. However, adequate genome resources for gaining insight into sex-determining mechanisms and establishing genetically resistant breeding systems for O. fasciatus are lacking. Here, we analyzed the entire genome of a female O. fasciatus fish using long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly. Findings: We assembled the O. fasciatus genome with a total of 245.0 Gb of raw reads that were generated using both Pacific Bioscience (PacBio) Sequel and Illumina HiSeq 2000 platforms. The final draft genome assembly was approximately 778.7 Mb, which reached a high level of continuity with a contig N50 of 2.1 Mb. The genome size was consistent with the estimated genome size (777.5 Mb) based on k-mer analysis. We combined Hi-C data with a draft genome assembly to generate chromosome-length scaffolds. Twenty-four scaffolds corresponding to the 24 chromosomes were assembled to a final size of 768.8 Mb with a contig N50 of 2.1 Mb and a scaffold N50 of 33.5 Mb using 1,372 contigs. The identified repeat sequences accounted for 33.9% of the entire genome, and 24 003 protein-coding genes with an average of 10.1 exons per gene were annotated using de novo methods, with RNA sequencing data and homologies to other teleosts. According to phylogenetic analysis using protein-coding genes, O. fasciatus is closely related to Larimichthys crocea, with O. fasciatus diverging from their common ancestor approximately 70.5-88.5 million years ago. Conclusions: We generated a high-quality draft genome for O. fasciatus using long-read PacBio sequencing technology, which represents the first chromosome-level reference genome for Oplegnathidae species. Assembly of this genome assists research into fish sex-determining mechanisms and can serve as a resource for accelerating genome-assisted improvements in resistant breeding systems.
KeywordOplegnathus fasciatus chromosome-level genome assembly Hi-C assembly sex-determining mechanism
DOI10.1093/gigascience/giz013
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[41506170] ; National Natural Science Foundation of China[31672672] ; National Natural Science Foundation of China[31872195] ; Shandong Province Key Research and Invention Program[2017GHY15102] ; Shandong Province Key Research and Invention Program[2017GHY15106] ; Qingdao Source Innovation Program[17-1-1-57-jch] ; Marine Fishery Institute of Zhejiang Province ; Key Laboratory of Mariculture and Enhancement of Zhejiang Province[2016KF002] ; National Key Research and Development Program[2018YFD0901204] ; STS project[KFZD-SW-106] ; STS project[ZSSD-019] ; Qingdao National Laboratory for Marine Science and Technology[2015ASKJ02] ; China Agriculture Research System[CARS-47]
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000466726800011
PublisherOXFORD UNIV PRESS
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/161377
Collection中国科学院海洋研究所
Corresponding AuthorLiu, Jing; Li, Jun
Affiliation1.Chinese Acad Sci, Inst Oceanol, 7 Nanhai Rd, Qingdao 266071, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, 7 Nanhai Rd, Qingdao 266071, Peoples R China
3.Chinese Acad Sci, Ctr Ocean Mega Sci, 7 Nanhai Rd, Qingdao 266071, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Corresponding Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Xiao, Yongshuang,Xiao, Zhizhong,Ma, Daoyuan,et al. Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae[J]. GIGASCIENCE,2019,8(3):8.
APA Xiao, Yongshuang,Xiao, Zhizhong,Ma, Daoyuan,Liu, Jing,&Li, Jun.(2019).Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae.GIGASCIENCE,8(3),8.
MLA Xiao, Yongshuang,et al."Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae".GIGASCIENCE 8.3(2019):8.
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