Cargando…
Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.)
BACKGROUND: Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenc...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298812/ https://www.ncbi.nlm.nih.gov/pubmed/32546133 http://dx.doi.org/10.1186/s12864-020-06805-6 |
_version_ | 1783547276582453248 |
---|---|
author | Yang, Zemao Dai, Zhigang Chen, Xiaojun Xie, Dongwei Tang, Qing Cheng, Chaohua Xu, Ying Deng, Canhui Liu, Chan Chen, Jiquan Su, Jianguang |
author_facet | Yang, Zemao Dai, Zhigang Chen, Xiaojun Xie, Dongwei Tang, Qing Cheng, Chaohua Xu, Ying Deng, Canhui Liu, Chan Chen, Jiquan Su, Jianguang |
author_sort | Yang, Zemao |
collection | PubMed |
description | BACKGROUND: Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS: There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION: We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops. |
format | Online Article Text |
id | pubmed-7298812 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-72988122020-06-17 Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) Yang, Zemao Dai, Zhigang Chen, Xiaojun Xie, Dongwei Tang, Qing Cheng, Chaohua Xu, Ying Deng, Canhui Liu, Chan Chen, Jiquan Su, Jianguang BMC Genomics Research Article BACKGROUND: Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS: There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION: We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops. BioMed Central 2020-06-16 /pmc/articles/PMC7298812/ /pubmed/32546133 http://dx.doi.org/10.1186/s12864-020-06805-6 Text en © The Author(s) 2020 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/. The Creative Commons Public Domain Dedication waiver (http://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 Yang, Zemao Dai, Zhigang Chen, Xiaojun Xie, Dongwei Tang, Qing Cheng, Chaohua Xu, Ying Deng, Canhui Liu, Chan Chen, Jiquan Su, Jianguang Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title | Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title_full | Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title_fullStr | Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title_full_unstemmed | Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title_short | Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.) |
title_sort | gene coexpression network analysis and tissue-specific profiling of gene expression in jute (corchorus capsularis l.) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7298812/ https://www.ncbi.nlm.nih.gov/pubmed/32546133 http://dx.doi.org/10.1186/s12864-020-06805-6 |
work_keys_str_mv | AT yangzemao genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT daizhigang genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT chenxiaojun genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT xiedongwei genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT tangqing genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT chengchaohua genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT xuying genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT dengcanhui genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT liuchan genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT chenjiquan genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl AT sujianguang genecoexpressionnetworkanalysisandtissuespecificprofilingofgeneexpressioninjutecorchoruscapsularisl |