Identification of stress-related genes by co-expression network analysis based on the improved turbot genome
Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present a...
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ftpubmed:oai:pubmedcentral.nih.gov:9243025 2023-05-15T18:15:48+02:00 Identification of stress-related genes by co-expression network analysis based on the improved turbot genome Xu, Xi-wen Zheng, Weiwei Meng, Zhen Xu, Wenteng Liu, Yingjie Chen, Songlin 2022-06-29 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243025/ https://doi.org/10.1038/s41597-022-01458-4 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243025/ http://dx.doi.org/10.1038/s41597-022-01458-4 © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . CC-BY Sci Data Data Descriptor Text 2022 ftpubmed https://doi.org/10.1038/s41597-022-01458-4 2022-07-03T01:06:24Z Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties. Text Scophthalmus maximus Turbot PubMed Central (PMC) Scientific Data 9 1 |
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Data Descriptor Xu, Xi-wen Zheng, Weiwei Meng, Zhen Xu, Wenteng Liu, Yingjie Chen, Songlin Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
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Data Descriptor |
description |
Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties. |
format |
Text |
author |
Xu, Xi-wen Zheng, Weiwei Meng, Zhen Xu, Wenteng Liu, Yingjie Chen, Songlin |
author_facet |
Xu, Xi-wen Zheng, Weiwei Meng, Zhen Xu, Wenteng Liu, Yingjie Chen, Songlin |
author_sort |
Xu, Xi-wen |
title |
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
title_short |
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
title_full |
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
title_fullStr |
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
title_full_unstemmed |
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
title_sort |
identification of stress-related genes by co-expression network analysis based on the improved turbot genome |
publisher |
Nature Publishing Group UK |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243025/ https://doi.org/10.1038/s41597-022-01458-4 |
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Scophthalmus maximus Turbot |
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Scophthalmus maximus Turbot |
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Sci Data |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243025/ http://dx.doi.org/10.1038/s41597-022-01458-4 |
op_rights |
© The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
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CC-BY |
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https://doi.org/10.1038/s41597-022-01458-4 |
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