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Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

BACKGROUND: Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic str...

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Autores principales: Di, Peng, Wang, Ping, Yan, Min, Han, Peng, Huang, Xinyi, Yin, Le, Yan, Yan, Xu, Yonghua, Wang, Yingping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600734/
https://www.ncbi.nlm.nih.gov/pubmed/34794386
http://dx.doi.org/10.1186/s12864-021-08145-5
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author Di, Peng
Wang, Ping
Yan, Min
Han, Peng
Huang, Xinyi
Yin, Le
Yan, Yan
Xu, Yonghua
Wang, Yingping
author_facet Di, Peng
Wang, Ping
Yan, Min
Han, Peng
Huang, Xinyi
Yin, Le
Yan, Yan
Xu, Yonghua
Wang, Yingping
author_sort Di, Peng
collection PubMed
description BACKGROUND: Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. RESULTS: In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. CONCLUSIONS: This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08145-5.
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spelling pubmed-86007342021-11-19 Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng Di, Peng Wang, Ping Yan, Min Han, Peng Huang, Xinyi Yin, Le Yan, Yan Xu, Yonghua Wang, Yingping BMC Genomics Research Article BACKGROUND: Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. RESULTS: In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. CONCLUSIONS: This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08145-5. BioMed Central 2021-11-18 /pmc/articles/PMC8600734/ /pubmed/34794386 http://dx.doi.org/10.1186/s12864-021-08145-5 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Di, Peng
Wang, Ping
Yan, Min
Han, Peng
Huang, Xinyi
Yin, Le
Yan, Yan
Xu, Yonghua
Wang, Yingping
Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title_full Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title_fullStr Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title_full_unstemmed Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title_short Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng
title_sort genome-wide characterization and analysis of wrky transcription factors in panax ginseng
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600734/
https://www.ncbi.nlm.nih.gov/pubmed/34794386
http://dx.doi.org/10.1186/s12864-021-08145-5
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