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dc.contributor.authorBlein, Thomas
dc.contributor.authorBalzergue, Coline
dc.contributor.authorRoulé, Thomas
dc.contributor.authorGabriel, Marc
dc.contributor.authorScalisi, Laetitia
dc.contributor.authorFrançois, Tracy
dc.contributor.authorSorin, Céline
dc.contributor.authorChrist, Aurélie
dc.contributor.authorGodon, Christian
dc.contributor.authorDelannoy, Etienne
dc.contributor.authorMartin-Magniette, Marie-Laure
dc.contributor.authorNussaume, Laurent
dc.contributor.authorHartmann, Caroline
dc.contributor.authorGautheret, Daniel
dc.contributor.authorDesnos, Thierry M.
dc.contributor.authorCrespi, Martin
dc.date.accessioned2020-05-19T12:10:06Z
dc.date.available2020-05-19T12:10:06Z
dc.date.issued2020-05-13
dc.date.submitted2020-04-15
dc.identifier.citationBlein, T., Balzergue, C., Roulé, T., Gabriel, M., Scalisi, L., François, T., … Crespi, M. (2020). Landscape of the non-coding transcriptome response of two Arabidopsis ecotypes to phosphate starvation. Plant Physiology, pp.00446.2020. doi:10.1104/pp.20.00446
dc.identifier.issn0032-0889
dc.identifier.issn1532-2548
dc.identifier.doi10.1104/pp.20.00446
dc.identifier.urihttp://hdl.handle.net/10754/662875
dc.description.abstractRoot architecture varies widely between species, and even between ecotypes of the same species, despite the strong conservation of the coding portion of their genomes. By contrast, non-coding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long non-coding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from Columbia (Col) and Landsberg erecta (Ler) ecotypes respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with siRNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Mis-regulation of several intergenic lncRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in Col. RNA-seq analysis following the deregulation of the lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the non-coding transcriptome identified ecotype-specific lncRNAs-mediated regulation in root apexes. The non-coding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.
dc.description.sponsorshipThis work was supported by grants from Agence Nationale pour la Recherche (ANR) RNAdapt (grant no. ANR-12-ADAP-0019), SPLISIL (grant no. ANR-16-CE12-0032) and grants of The King Abdulla University of Science and Technology (KAUST) International Program OCRF-2014-CRG4. This work has benefited from a French State grant (Saclay Plant Sciences, reference n° ANR-17-EUR-0007, EUR SPS-GSR) managed by the French National Research Agency under an Investments for the Future program (reference n°ANR-11-IDEX-0003-02).
dc.publisherAmerican Society of Plant Biologists (ASPB)
dc.relation.urlhttp://www.plantphysiol.org/lookup/doi/10.1104/pp.20.00446
dc.rightsArchived with thanks to Plant Physiology
dc.titleLandscape of the non-coding transcriptome response of two Arabidopsis ecotypes to phosphate starvation
dc.typeArticle
dc.identifier.journalPlant Physiology
dc.eprint.versionPost-print
dc.contributor.institutionInstitute of Plant Sciences Paris Saclay (IPS2) CITY: Gif-sur-Yvette France [FR]
dc.contributor.institutionLaboratoire de Biologie Végétale et Microbiologie Environnementale, Unité mixte de recherche 7265 CNRS, CEA, Université Aix-Marseille; Institut de Biosciences et Biotechn CITY: Saint-Paul-lez-Durance France [FR]
dc.contributor.institutionInstitute for Integrative Biology of the Cell (I2BC) CITY: Gif-sur-Yvette France [FR]
dc.contributor.institutionInstitute of Plant Sciences of Paris-Saclay CITY: Gif sur Yvette France [FR]
dc.contributor.institutionConsorci CSIC-IRTA-UAB-UB CITY: Bellaterra (Cerdanyola del Valles) Spain [ES]
dc.contributor.institutionCommissariat � l'Energie Atomique CITY: St Paul-lez-Durance France [FR]
dc.contributor.institutionInstitut de Science des Plantes de Paris Saclay CITY: Orsay France [FR]
dc.contributor.institutionIPS2 CITY: Gif-sur-Yvette France [FR]
dc.contributor.institutionCommissanat a l'Energie Atomique Laboratoire du Metabolisme Carbone, Departement d'Ecophysiologie Vegetale et Microbiologie, Centre de Cadarache CITY: 13108 Saint Paul Lez Durance Cedex POSTAL_CODE: n/a France [FR]
dc.contributor.institutionCommissariat � l'Energie Atomique CEA cadarache, DEVM/LBDP, Bat 178 CITY: St Paul-lez-Durance POSTAL_CODE: 13108 France [FR]
dc.contributor.institutionInstitute of Plant Sciences of Paris-Saclay CITY: Gif sur Yvette POSTAL_CODE: 91190 France [FR]
dc.identifier.pagespp.00446.2020
kaust.grant.numberCRG4
kaust.grant.numberOCRF-2014-CRG
dc.date.accepted2020-04-30
dc.date.published-online2020-05-13
dc.date.published-print2020-07


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