Cargando…
Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress
To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mappe...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776286/ https://www.ncbi.nlm.nih.gov/pubmed/26935041 http://dx.doi.org/10.1038/srep22583 |
_version_ | 1782419132191342592 |
---|---|
author | Zorrilla-Fontanesi, Yasmín Rouard, Mathieu Cenci, Alberto Kissel, Ewaut Do, Hien Dubois, Emeric Nidelet, Sabine Roux, Nicolas Swennen, Rony Carpentier, Sebastien Christian |
author_facet | Zorrilla-Fontanesi, Yasmín Rouard, Mathieu Cenci, Alberto Kissel, Ewaut Do, Hien Dubois, Emeric Nidelet, Sabine Roux, Nicolas Swennen, Rony Carpentier, Sebastien Christian |
author_sort | Zorrilla-Fontanesi, Yasmín |
collection | PubMed |
description | To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress. |
format | Online Article Text |
id | pubmed-4776286 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-47762862016-03-09 Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress Zorrilla-Fontanesi, Yasmín Rouard, Mathieu Cenci, Alberto Kissel, Ewaut Do, Hien Dubois, Emeric Nidelet, Sabine Roux, Nicolas Swennen, Rony Carpentier, Sebastien Christian Sci Rep Article To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress. Nature Publishing Group 2016-03-03 /pmc/articles/PMC4776286/ /pubmed/26935041 http://dx.doi.org/10.1038/srep22583 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Zorrilla-Fontanesi, Yasmín Rouard, Mathieu Cenci, Alberto Kissel, Ewaut Do, Hien Dubois, Emeric Nidelet, Sabine Roux, Nicolas Swennen, Rony Carpentier, Sebastien Christian Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title | Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title_full | Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title_fullStr | Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title_full_unstemmed | Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title_short | Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
title_sort | differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776286/ https://www.ncbi.nlm.nih.gov/pubmed/26935041 http://dx.doi.org/10.1038/srep22583 |
work_keys_str_mv | AT zorrillafontanesiyasmin differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT rouardmathieu differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT cencialberto differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT kisselewaut differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT dohien differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT duboisemeric differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT nideletsabine differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT rouxnicolas differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT swennenrony differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress AT carpentiersebastienchristian differentialroottranscriptomicsinapolyploidnonmodelcroptheimportanceofrespirationduringosmoticstress |