Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration

doi:10.1038/s41597-023-02699-7

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
发表期刊	SCIENTIFIC DATA
卷号	10 期号:1 页码:16
通讯作者	Liu, Jing(jliu@qdio.ac.cn) ; Li, Jun(junli@qdio.ac.cn)
摘要	Sciaenops 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.
DOI	10.1038/s41597-023-02699-7
收录类别	SCI
语种	英语
资助项目	This 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研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:001101168600001
出版者	NATURE PORTFOLIO
WOS关键词	DE-NOVO IDENTIFICATION ; SCIAENOPS-OCELLATUS ; READ ALIGNMENT ; TRANSCRIPTOME ; DATABASE ; PROGRAM ; GROWTH ; OSMOREGULATION ; EXPRESSION ; STRINGTIE
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/184005
专题	中国科学院海洋研究所
通讯作者	Liu, Jing; Li, Jun
作者单位	Chinese Acad Sci, Inst Oceanol, Ctr Ocean Mega Sci, Qingdao, Peoples R China
第一作者单位	中国科学院海洋研究所
通讯作者单位	中国科学院海洋研究所
推荐引用方式 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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