Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration
Abstract 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 nov...
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ftdoajarticles:oai:doaj.org/article:8f9676b0ce8c417aa62aabbe5faef5ae 2023-12-31T10:22:25+01:00 Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration Yongshuang Xiao Jing Liu Jiehong Wei Zhizhong Xiao Jun Li Yuting Ma 2023-11-01T00:00:00Z https://doi.org/10.1038/s41597-023-02699-7 https://doaj.org/article/8f9676b0ce8c417aa62aabbe5faef5ae EN eng Nature Portfolio https://doi.org/10.1038/s41597-023-02699-7 https://doaj.org/toc/2052-4463 doi:10.1038/s41597-023-02699-7 2052-4463 https://doaj.org/article/8f9676b0ce8c417aa62aabbe5faef5ae Scientific Data, Vol 10, Iss 1, Pp 1-16 (2023) Science Q article 2023 ftdoajarticles https://doi.org/10.1038/s41597-023-02699-7 2023-12-03T01:44:04Z Abstract 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. Article in Journal/Newspaper Red drum Sciaenops ocellatus Directory of Open Access Journals: DOAJ Articles Scientific Data 10 1 |
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Science Q Yongshuang Xiao Jing Liu Jiehong Wei Zhizhong Xiao Jun Li Yuting Ma Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration |
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Abstract 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 |
Article in Journal/Newspaper |
author |
Yongshuang Xiao Jing Liu Jiehong Wei Zhizhong Xiao Jun Li Yuting Ma |
author_facet |
Yongshuang Xiao Jing Liu Jiehong Wei Zhizhong Xiao Jun Li Yuting Ma |
author_sort |
Yongshuang Xiao |
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 |
https://doi.org/10.1038/s41597-023-02699-7 https://doaj.org/article/8f9676b0ce8c417aa62aabbe5faef5ae |
genre |
Red drum Sciaenops ocellatus |
genre_facet |
Red drum Sciaenops ocellatus |
op_source |
Scientific Data, Vol 10, Iss 1, Pp 1-16 (2023) |
op_relation |
https://doi.org/10.1038/s41597-023-02699-7 https://doaj.org/toc/2052-4463 doi:10.1038/s41597-023-02699-7 2052-4463 https://doaj.org/article/8f9676b0ce8c417aa62aabbe5faef5ae |
op_doi |
https://doi.org/10.1038/s41597-023-02699-7 |
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Scientific Data |
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