RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings
Helictotrichon virescens is a perennial herbaceous plant with a life expectancy of about 10 years. It has high cold and heat resistance and can successfully survive over winter in the habitats with a temperature range of −25 to 25°C. Therefore, this study aimed to identify the key genes regulating l...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9478469/ https://www.ncbi.nlm.nih.gov/pubmed/36119608 http://dx.doi.org/10.3389/fpls.2022.938859 |
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author | Cheng, Mingjun Pan, Zeyang Cui, Kuoshu Zheng, Junjun Luo, Xuan Chen, Youjun Yang, Tao Wang, Hui Li, Xiaofeng Zhou, Yang Lei, Xiong Li, Yingzheng Zhang, Ruizhen Iqbal, Muhammad Zafar He, Ruyu |
author_facet | Cheng, Mingjun Pan, Zeyang Cui, Kuoshu Zheng, Junjun Luo, Xuan Chen, Youjun Yang, Tao Wang, Hui Li, Xiaofeng Zhou, Yang Lei, Xiong Li, Yingzheng Zhang, Ruizhen Iqbal, Muhammad Zafar He, Ruyu |
author_sort | Cheng, Mingjun |
collection | PubMed |
description | Helictotrichon virescens is a perennial herbaceous plant with a life expectancy of about 10 years. It has high cold and heat resistance and can successfully survive over winter in the habitats with a temperature range of −25 to 25°C. Therefore, this study aimed to identify the key genes regulating low-temperature stress responses in H. virescens and analyze cold tolerant at molecular level. This study used RNA sequencing (RNA-Seq) and weighted gene co-expression network analysis (WGCNA) to identify the hub genes associated with cold tolerance in H. virescens. RT-PCR was conducted, homologous genes were identified, and related bioinformatics were analyzed to verify the identified hub genes. Moreover, WGCNA analysis showed that only the brown module had the highest correlation with the active-oxygen scavenging enzymes [peroxide (POD), superoxide dismutase (SOD), and catalase (CAT)]. The expression levels of three hub genes in the brown module (Cluster-37118.47362, cluster-37118.47713, and cluster-37118.66740) were significantly higher under low-temperature stress than those under control conditions. Furthermore, gene ontology (GO) and KEGG annotations showed that the three hub genes were mainly enriched in the metabolism pathways of sphingolipids, selenocompounds, glyoxylate, and dicarboxylate, carotenoids biosynthesis, and other biological pathways. The results of this study also showed that the subcellular localization prediction results showed that the cold tolerance hub genes were all localized to the plasma membrane. By constructing a protein interaction network, it was found that the hub gene Cluster-37118.66740 interacted with Sb09g003460.1 and Sb04g020180.1 proteins in Sorghum bicolor. By constructing phylogenetic trees of the four species of H. virescens, Sorghum bicolo, Oryza sativa Japonica, and Arabidopsis thaliana, the results showed that, the hub gene Cluster 37118.66740 (of H. virescens) and Os03g0340500 (of Oryza sativa Japonica) belonged to the same ancestral branch and were in the same subfamily. Thus, this study provides methodology and guidance to identify the cold tolerance genes for other herbage and their cold tolerant molecular mechanisms at molecular level. |
format | Online Article Text |
id | pubmed-9478469 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94784692022-09-17 RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings Cheng, Mingjun Pan, Zeyang Cui, Kuoshu Zheng, Junjun Luo, Xuan Chen, Youjun Yang, Tao Wang, Hui Li, Xiaofeng Zhou, Yang Lei, Xiong Li, Yingzheng Zhang, Ruizhen Iqbal, Muhammad Zafar He, Ruyu Front Plant Sci Plant Science Helictotrichon virescens is a perennial herbaceous plant with a life expectancy of about 10 years. It has high cold and heat resistance and can successfully survive over winter in the habitats with a temperature range of −25 to 25°C. Therefore, this study aimed to identify the key genes regulating low-temperature stress responses in H. virescens and analyze cold tolerant at molecular level. This study used RNA sequencing (RNA-Seq) and weighted gene co-expression network analysis (WGCNA) to identify the hub genes associated with cold tolerance in H. virescens. RT-PCR was conducted, homologous genes were identified, and related bioinformatics were analyzed to verify the identified hub genes. Moreover, WGCNA analysis showed that only the brown module had the highest correlation with the active-oxygen scavenging enzymes [peroxide (POD), superoxide dismutase (SOD), and catalase (CAT)]. The expression levels of three hub genes in the brown module (Cluster-37118.47362, cluster-37118.47713, and cluster-37118.66740) were significantly higher under low-temperature stress than those under control conditions. Furthermore, gene ontology (GO) and KEGG annotations showed that the three hub genes were mainly enriched in the metabolism pathways of sphingolipids, selenocompounds, glyoxylate, and dicarboxylate, carotenoids biosynthesis, and other biological pathways. The results of this study also showed that the subcellular localization prediction results showed that the cold tolerance hub genes were all localized to the plasma membrane. By constructing a protein interaction network, it was found that the hub gene Cluster-37118.66740 interacted with Sb09g003460.1 and Sb04g020180.1 proteins in Sorghum bicolor. By constructing phylogenetic trees of the four species of H. virescens, Sorghum bicolo, Oryza sativa Japonica, and Arabidopsis thaliana, the results showed that, the hub gene Cluster 37118.66740 (of H. virescens) and Os03g0340500 (of Oryza sativa Japonica) belonged to the same ancestral branch and were in the same subfamily. Thus, this study provides methodology and guidance to identify the cold tolerance genes for other herbage and their cold tolerant molecular mechanisms at molecular level. Frontiers Media S.A. 2022-09-02 /pmc/articles/PMC9478469/ /pubmed/36119608 http://dx.doi.org/10.3389/fpls.2022.938859 Text en Copyright © 2022 Cheng, Pan, Cui, Zheng, Luo, Chen, Yang, Wang, Li, Zhou, Lei, Li, Zhang, Iqbal and He. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Cheng, Mingjun Pan, Zeyang Cui, Kuoshu Zheng, Junjun Luo, Xuan Chen, Youjun Yang, Tao Wang, Hui Li, Xiaofeng Zhou, Yang Lei, Xiong Li, Yingzheng Zhang, Ruizhen Iqbal, Muhammad Zafar He, Ruyu RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title | RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title_full | RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title_fullStr | RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title_full_unstemmed | RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title_short | RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings |
title_sort | rna sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in helictotrichon virescens seedlings |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9478469/ https://www.ncbi.nlm.nih.gov/pubmed/36119608 http://dx.doi.org/10.3389/fpls.2022.938859 |
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