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Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa

BACKGROUND: Paulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane sulfonate (MMS) treatment. To completely understand the gene expression profiles...

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Autores principales: Fan, Guoqiang, Cao, Xibing, Niu, Suyan, Deng, Minjie, Zhao, Zhenli, Dong, Yanpeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634154/
https://www.ncbi.nlm.nih.gov/pubmed/26537848
http://dx.doi.org/10.1186/s12864-015-2074-3
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author Fan, Guoqiang
Cao, Xibing
Niu, Suyan
Deng, Minjie
Zhao, Zhenli
Dong, Yanpeng
author_facet Fan, Guoqiang
Cao, Xibing
Niu, Suyan
Deng, Minjie
Zhao, Zhenli
Dong, Yanpeng
author_sort Fan, Guoqiang
collection PubMed
description BACKGROUND: Paulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane sulfonate (MMS) treatment. To completely understand the gene expression profiles of the Paulownia-phytoplasma interaction, three high-throughput sequencing technologies were used to investigate changes of gene expression and microRNAs (miRNAs) in healthy Paulownia tomentosa plantlets, PaWB-infected plantlets, and PaWB-infected plantlets treated with 60 mg · L(−1) MMS. METHODS: Transcriptome, miRNAs and degradome sequencing were performed to explore the global gene expression profiles in the process of Paulownia tomentosa with phytoplasma infection. RESULTS: A total of 98,714 all-unigenes, 62 conserved miRNAs, and 35 novel miRNAs were obtained, among which 902 differentially expressed genes (DEGs) and 24 miRNAs were found to be associated with PaWB disease. Subsequently, the target genes of these miRNAs were predicted by degradome sequencing. Interestingly, we found that 19 target genes of these differentially expressed miRNAs were among the 902 DEGs. The targets of pau-miR156g, pau-miR403, and pau-miR166c were significantly up-regulated in the P. tomentosa plantlets infected with phytoplasma. Interaction of miRNA -target genes mediated gene expression related to PaWB were identified. CONCLUSIONS: The results elucidated the possible roles of the regulation of genes and miRNAs in the Paulownia-phytoplasma interaction, which will enrich our understanding of the mechanisms of PaWB disease in this plant. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2074-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-46341542015-11-06 Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa Fan, Guoqiang Cao, Xibing Niu, Suyan Deng, Minjie Zhao, Zhenli Dong, Yanpeng BMC Genomics Research Article BACKGROUND: Paulownia witches’ broom (PaWB) is a fatal disease of Paulownia caused by a phytoplasma. In previous studies, we found that plants with PaWB symptoms would revert to a healthy morphology after methyl methane sulfonate (MMS) treatment. To completely understand the gene expression profiles of the Paulownia-phytoplasma interaction, three high-throughput sequencing technologies were used to investigate changes of gene expression and microRNAs (miRNAs) in healthy Paulownia tomentosa plantlets, PaWB-infected plantlets, and PaWB-infected plantlets treated with 60 mg · L(−1) MMS. METHODS: Transcriptome, miRNAs and degradome sequencing were performed to explore the global gene expression profiles in the process of Paulownia tomentosa with phytoplasma infection. RESULTS: A total of 98,714 all-unigenes, 62 conserved miRNAs, and 35 novel miRNAs were obtained, among which 902 differentially expressed genes (DEGs) and 24 miRNAs were found to be associated with PaWB disease. Subsequently, the target genes of these miRNAs were predicted by degradome sequencing. Interestingly, we found that 19 target genes of these differentially expressed miRNAs were among the 902 DEGs. The targets of pau-miR156g, pau-miR403, and pau-miR166c were significantly up-regulated in the P. tomentosa plantlets infected with phytoplasma. Interaction of miRNA -target genes mediated gene expression related to PaWB were identified. CONCLUSIONS: The results elucidated the possible roles of the regulation of genes and miRNAs in the Paulownia-phytoplasma interaction, which will enrich our understanding of the mechanisms of PaWB disease in this plant. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2074-3) contains supplementary material, which is available to authorized users. BioMed Central 2015-11-04 /pmc/articles/PMC4634154/ /pubmed/26537848 http://dx.doi.org/10.1186/s12864-015-2074-3 Text en © Fan et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 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.
spellingShingle Research Article
Fan, Guoqiang
Cao, Xibing
Niu, Suyan
Deng, Minjie
Zhao, Zhenli
Dong, Yanpeng
Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title_full Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title_fullStr Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title_full_unstemmed Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title_short Transcriptome, microRNA, and degradome analyses of the gene expression of Paulownia with phytoplamsa
title_sort transcriptome, microrna, and degradome analyses of the gene expression of paulownia with phytoplamsa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634154/
https://www.ncbi.nlm.nih.gov/pubmed/26537848
http://dx.doi.org/10.1186/s12864-015-2074-3
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