IOCAS-IR
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration
Xiao, Yongshuang; Liu, Jing; Wei, Jiehong; Xiao, Zhizhong; Li, Jun; Ma, Yuting
2023-11-07
Source PublicationSCIENTIFIC DATA
Volume10Issue:1Pages:16
Corresponding AuthorLiu, Jing(jliu@qdio.ac.cn) ; Li, Jun(junli@qdio.ac.cn)
AbstractSciaenops ocellatus is among the most important artificially introduced farmed fish across 11 countries and regions. However, the frequent occurrence of extreme weather events and breeding escapes have placed great pressure on local marine biodiversity and ecosystems. We reported the de novo assembly and annotation with a contig N50 of 28.30 Mb using PacBio HiFi sequencing and Hi-C technologies, which resulted in a 283-fold increase in contig N50 length and improvement in continuity and quality in complex repetitive region for S. ocellatus compared to the previous version. In total, 257.36 Mb of repetitive sequences accounted for 35.48% of the genome, and 22,845 protein-coding genes associated with a BUSCO value of 98.32%, were identified by genome annotation. Moreover, 54 hub genes rapidly responding to hypoosmotic stress were identified by WGCNA. The high-quality chromosome-scale S. ocellatus genome and candidate resistance-related gene sets will not only provide a genomic basis for genetic improvement via molecular breeding, but will also lay an important foundation for investigating the molecular regulation of rapid responses to stress.
DOI10.1038/s41597-023-02699-7
Indexed BySCI
Language英语
Funding ProjectThis work was supported by Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDB42000000), National Natural Science Foundation of China (No. 42276107; No. 32270472); Biodiversity Conservation Strategy, CAS Strategic Biological Res[XDB42000000] ; Strategic Priority Research Program of the Chinese Academy of Sciences[42276107] ; Strategic Priority Research Program of the Chinese Academy of Sciences[32270472] ; National Natural Science Foundation of China[ZSSD-019] ; Biodiversity Conservation Strategy, CAS Strategic Biological Resources Service Network Program[COMS2020Q05] ; Key Deployment Project of Center for Ocean Mega-Science, Chinese Academy of Sciences[2022YFC3103600] ; National Key Research and Development Program
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:001101168600001
PublisherNATURE PORTFOLIO
WOS KeywordDE-NOVO IDENTIFICATION ; SCIAENOPS-OCELLATUS ; READ ALIGNMENT ; TRANSCRIPTOME ; DATABASE ; PROGRAM ; GROWTH ; OSMOREGULATION ; EXPRESSION ; STRINGTIE
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Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/184005
Collection中国科学院海洋研究所
Corresponding AuthorLiu, Jing; Li, Jun
AffiliationChinese Acad Sci, Inst Oceanol, Ctr Ocean Mega Sci, Qingdao, 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,Liu, Jing,Wei, Jiehong,et al. Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration[J]. SCIENTIFIC DATA,2023,10(1):16.
APA Xiao, Yongshuang,Liu, Jing,Wei, Jiehong,Xiao, Zhizhong,Li, Jun,&Ma, Yuting.(2023).Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration.SCIENTIFIC DATA,10(1),16.
MLA Xiao, Yongshuang,et al."Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration".SCIENTIFIC DATA 10.1(2023):16.
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