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mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage

The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H(2)O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obt...

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Autores principales: Zhang, Xueyan, Yao, Dongxia, Wang, Qianhua, Xu, Wenying, Wei, Qiang, Wang, Chunchao, Liu, Chuanliang, Zhang, Chaojun, Yan, Hong, Ling, Yi, Su, Zhen, Li, Fuguang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557298/
https://www.ncbi.nlm.nih.gov/pubmed/23382961
http://dx.doi.org/10.1371/journal.pone.0054762
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author Zhang, Xueyan
Yao, Dongxia
Wang, Qianhua
Xu, Wenying
Wei, Qiang
Wang, Chunchao
Liu, Chuanliang
Zhang, Chaojun
Yan, Hong
Ling, Yi
Su, Zhen
Li, Fuguang
author_facet Zhang, Xueyan
Yao, Dongxia
Wang, Qianhua
Xu, Wenying
Wei, Qiang
Wang, Chunchao
Liu, Chuanliang
Zhang, Chaojun
Yan, Hong
Ling, Yi
Su, Zhen
Li, Fuguang
author_sort Zhang, Xueyan
collection PubMed
description The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H(2)O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.
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spelling pubmed-35572982013-02-04 mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage Zhang, Xueyan Yao, Dongxia Wang, Qianhua Xu, Wenying Wei, Qiang Wang, Chunchao Liu, Chuanliang Zhang, Chaojun Yan, Hong Ling, Yi Su, Zhen Li, Fuguang PLoS One Research Article The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H(2)O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species. Public Library of Science 2013-01-28 /pmc/articles/PMC3557298/ /pubmed/23382961 http://dx.doi.org/10.1371/journal.pone.0054762 Text en © 2013 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Zhang, Xueyan
Yao, Dongxia
Wang, Qianhua
Xu, Wenying
Wei, Qiang
Wang, Chunchao
Liu, Chuanliang
Zhang, Chaojun
Yan, Hong
Ling, Yi
Su, Zhen
Li, Fuguang
mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title_full mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title_fullStr mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title_full_unstemmed mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title_short mRNA-seq Analysis of the Gossypium arboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage
title_sort mrna-seq analysis of the gossypium arboreum transcriptome reveals tissue selective signaling in response to water stress during seedling stage
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3557298/
https://www.ncbi.nlm.nih.gov/pubmed/23382961
http://dx.doi.org/10.1371/journal.pone.0054762
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