Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration
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 assembl...
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Online Access: | http://ir.qdio.ac.cn/handle/337002/184004 http://ir.qdio.ac.cn/handle/337002/184005 https://doi.org/10.1038/s41597-023-02699-7 |
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/184005 2024-05-12T08:10:24+00:00 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 http://ir.qdio.ac.cn/handle/337002/184004 http://ir.qdio.ac.cn/handle/337002/184005 https://doi.org/10.1038/s41597-023-02699-7 英语 eng NATURE PORTFOLIO SCIENTIFIC DATA http://ir.qdio.ac.cn/handle/337002/184004 http://ir.qdio.ac.cn/handle/337002/184005 doi:10.1038/s41597-023-02699-7 Science & Technology - Other Topics Multidisciplinary Sciences DE-NOVO IDENTIFICATION SCIAENOPS-OCELLATUS READ ALIGNMENT TRANSCRIPTOME DATABASE PROGRAM GROWTH OSMOREGULATION EXPRESSION STRINGTIE 期刊论文 2023 ftchinacasciocas https://doi.org/10.1038/s41597-023-02699-7 2024-04-14T23:52:16Z 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. Report Red drum Sciaenops ocellatus Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Scientific Data 10 1 |
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Open Polar |
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Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
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ftchinacasciocas |
language |
English |
topic |
Science & Technology - Other Topics Multidisciplinary Sciences DE-NOVO IDENTIFICATION SCIAENOPS-OCELLATUS READ ALIGNMENT TRANSCRIPTOME DATABASE PROGRAM GROWTH OSMOREGULATION EXPRESSION STRINGTIE |
spellingShingle |
Science & Technology - Other Topics Multidisciplinary Sciences DE-NOVO IDENTIFICATION SCIAENOPS-OCELLATUS READ ALIGNMENT TRANSCRIPTOME DATABASE PROGRAM GROWTH OSMOREGULATION EXPRESSION STRINGTIE Xiao, Yongshuang Liu, Jing Wei, Jiehong Xiao, Zhizhong Li, Jun Ma, Yuting Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
topic_facet |
Science & Technology - Other Topics Multidisciplinary Sciences DE-NOVO IDENTIFICATION SCIAENOPS-OCELLATUS READ ALIGNMENT TRANSCRIPTOME DATABASE PROGRAM GROWTH OSMOREGULATION EXPRESSION STRINGTIE |
description |
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. |
format |
Report |
author |
Xiao, Yongshuang Liu, Jing Wei, Jiehong Xiao, Zhizhong Li, Jun Ma, Yuting |
author_facet |
Xiao, Yongshuang Liu, Jing Wei, Jiehong Xiao, Zhizhong Li, Jun Ma, Yuting |
author_sort |
Xiao, Yongshuang |
title |
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
title_short |
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
title_full |
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
title_fullStr |
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
title_full_unstemmed |
Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
title_sort |
improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
publisher |
NATURE PORTFOLIO |
publishDate |
2023 |
url |
http://ir.qdio.ac.cn/handle/337002/184004 http://ir.qdio.ac.cn/handle/337002/184005 https://doi.org/10.1038/s41597-023-02699-7 |
genre |
Red drum Sciaenops ocellatus |
genre_facet |
Red drum Sciaenops ocellatus |
op_relation |
SCIENTIFIC DATA http://ir.qdio.ac.cn/handle/337002/184004 http://ir.qdio.ac.cn/handle/337002/184005 doi:10.1038/s41597-023-02699-7 |
op_doi |
https://doi.org/10.1038/s41597-023-02699-7 |
container_title |
Scientific Data |
container_volume |
10 |
container_issue |
1 |
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1798853843942899712 |