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Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)

BACKGROUND: Plant microRNAs (miRNAs) are involved in various biological pathways and stress responses as negative regulators at the posttranscriptional level. Abscisic acid (ABA) is a key signaling molecule that mediates plant stress response by activating many stress-related genes. Although some mi...

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Autores principales: Cheng, Hai-Yang, Wang, Yan, Tao, Xiang, Fan, Yan-Fen, Dai, Ya, Yang, Hong, Ma, Xin-Rong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891822/
https://www.ncbi.nlm.nih.gov/pubmed/27260799
http://dx.doi.org/10.1186/s12864-016-2591-8
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author Cheng, Hai-Yang
Wang, Yan
Tao, Xiang
Fan, Yan-Fen
Dai, Ya
Yang, Hong
Ma, Xin-Rong
author_facet Cheng, Hai-Yang
Wang, Yan
Tao, Xiang
Fan, Yan-Fen
Dai, Ya
Yang, Hong
Ma, Xin-Rong
author_sort Cheng, Hai-Yang
collection PubMed
description BACKGROUND: Plant microRNAs (miRNAs) are involved in various biological pathways and stress responses as negative regulators at the posttranscriptional level. Abscisic acid (ABA) is a key signaling molecule that mediates plant stress response by activating many stress-related genes. Although some miRNAs in plants are previously identified to respond to ABA, a comprehensive profile of ABA-responsive miRNAs has not yet been elucidated. RESULTS: Here, we identified miRNAs responding to exogenous application of ABA, and their predicted target genes in the model plant organism tomato (Solanum lycopersicum). Deep sequencing of small RNAs from ABA-treated and untreated tomatoes revealed that miRNAs can be up- or down-regulated upon treatment with ABA. A total of 1067 miRNAs were detected (including 365 known and 702 candidate novel miRNAs), of those, 416 miRNAs which had an abundance over two TPM (transcripts per million) were selected for differential expression analysis. We identified 269 (180 known and 89 novel) miRNAs that respond to exogenous ABA treatment with a change in expression level of |log(2)FC|≥0.25. 136 of these miRNAs (90 known and 46 novel) were expressed at significantly different levels |log(2)FC|≥1 between treatments. Furthermore, stem-loop RT-PCR was applied to validate the RNA-seq data. Target prediction and analysis of the corresponding ABA-responsive transcriptome data uncovered that differentially expressed miRNAs are involved in condition stress and pathogen resistance, growth and development. Among them, approximately 90 miRNAs were predicted to target transcription factors and pathogen resistance genes. Some miRNAs had functional overlap in biotic and abiotic stress. Most of these miRNAs were down-regulated following exposure to exogenous ABA, while their related target genes were inversely up-regulated, which is consistent with their negative regulatory role in gene expression. CONCLUSIONS: Exogenous ABA application influences the composition and expression level of tomato miRNAs. ABA mainly down-regulates miRNAs that their target genes involve in abiotic stress adaption and disease resistance. ABA might increase expression of stress-related genes via miRNA-mediated posttranscriptional regulation, and our results indicate that ABA treatment has the potential to improve both abiotic stress tolerance and pathogen resistance. This study presents a comprehensive profile of ABA-regulated miRNAs in the tomato, and provides a robust database for further investigation of ABA regulatory mechanisms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2591-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-48918222016-06-04 Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum) Cheng, Hai-Yang Wang, Yan Tao, Xiang Fan, Yan-Fen Dai, Ya Yang, Hong Ma, Xin-Rong BMC Genomics Research Article BACKGROUND: Plant microRNAs (miRNAs) are involved in various biological pathways and stress responses as negative regulators at the posttranscriptional level. Abscisic acid (ABA) is a key signaling molecule that mediates plant stress response by activating many stress-related genes. Although some miRNAs in plants are previously identified to respond to ABA, a comprehensive profile of ABA-responsive miRNAs has not yet been elucidated. RESULTS: Here, we identified miRNAs responding to exogenous application of ABA, and their predicted target genes in the model plant organism tomato (Solanum lycopersicum). Deep sequencing of small RNAs from ABA-treated and untreated tomatoes revealed that miRNAs can be up- or down-regulated upon treatment with ABA. A total of 1067 miRNAs were detected (including 365 known and 702 candidate novel miRNAs), of those, 416 miRNAs which had an abundance over two TPM (transcripts per million) were selected for differential expression analysis. We identified 269 (180 known and 89 novel) miRNAs that respond to exogenous ABA treatment with a change in expression level of |log(2)FC|≥0.25. 136 of these miRNAs (90 known and 46 novel) were expressed at significantly different levels |log(2)FC|≥1 between treatments. Furthermore, stem-loop RT-PCR was applied to validate the RNA-seq data. Target prediction and analysis of the corresponding ABA-responsive transcriptome data uncovered that differentially expressed miRNAs are involved in condition stress and pathogen resistance, growth and development. Among them, approximately 90 miRNAs were predicted to target transcription factors and pathogen resistance genes. Some miRNAs had functional overlap in biotic and abiotic stress. Most of these miRNAs were down-regulated following exposure to exogenous ABA, while their related target genes were inversely up-regulated, which is consistent with their negative regulatory role in gene expression. CONCLUSIONS: Exogenous ABA application influences the composition and expression level of tomato miRNAs. ABA mainly down-regulates miRNAs that their target genes involve in abiotic stress adaption and disease resistance. ABA might increase expression of stress-related genes via miRNA-mediated posttranscriptional regulation, and our results indicate that ABA treatment has the potential to improve both abiotic stress tolerance and pathogen resistance. This study presents a comprehensive profile of ABA-regulated miRNAs in the tomato, and provides a robust database for further investigation of ABA regulatory mechanisms. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2591-8) contains supplementary material, which is available to authorized users. BioMed Central 2016-06-03 /pmc/articles/PMC4891822/ /pubmed/27260799 http://dx.doi.org/10.1186/s12864-016-2591-8 Text en © Cheng et al. 2016 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
Cheng, Hai-Yang
Wang, Yan
Tao, Xiang
Fan, Yan-Fen
Dai, Ya
Yang, Hong
Ma, Xin-Rong
Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title_full Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title_fullStr Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title_full_unstemmed Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title_short Genomic profiling of exogenous abscisic acid-responsive microRNAs in tomato (Solanum lycopersicum)
title_sort genomic profiling of exogenous abscisic acid-responsive micrornas in tomato (solanum lycopersicum)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891822/
https://www.ncbi.nlm.nih.gov/pubmed/27260799
http://dx.doi.org/10.1186/s12864-016-2591-8
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