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Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation

Thomas Blein, Coline Balzergue, Thomas Roulé, Marc Gabriel, Laetitia Scalisi, Tracy François, Céline Sorin, Aurélie Christ, Christian Godon, Etienne Delannoy, Marie-Laure Martin-Magniette, Laurent Nussaume, Caroline Hartmann, Daniel Gautheret, Thierry Desnos, Martin Crespi
Thomas Blein
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Coline Balzergue
cAix Marseille University, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
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Thomas Roulé
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Marc Gabriel
eInstitute for Integrative Biology of the Cell, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Université Paris Sud, 91198 Gif sur Yvette, France
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Laetitia Scalisi
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Tracy François
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Céline Sorin
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Aurélie Christ
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Christian Godon
cAix Marseille University, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
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Etienne Delannoy
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Marie-Laure Martin-Magniette
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
dUnité Mixte de Recherche MIA-Paris (UMR MIA-Paris), AgroParisTech, Institut National de la Recherche Agronomique, Université Paris-Saclay, 75005 Paris, France
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Laurent Nussaume
cAix Marseille University, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
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Caroline Hartmann
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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Daniel Gautheret
eInstitute for Integrative Biology of the Cell, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Université Paris Sud, 91198 Gif sur Yvette, France
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Thierry Desnos
cAix Marseille University, Commisariat à l’Énergie Atomique, Centre Nationale de la Recherche, Bioscience and Biotechnology Institute of Aix-Marseilles, Unité Mixte de Recherche 7265 Signalisation pour l'Adaptation des Végétaux à leur Environnement (UMR7265 SAVE), 13108 Saint Paul-Lez-Durance, France
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Martin Crespi
aInstitute of Plant Sciences Paris-Saclay, Centre Nationale de la Recherche, Institut National de la Recherche Agronomique, Université Evry, Université Paris-Saclay, 91405 Orsay, France
bInstitute of Plant Sciences Paris-Saclay, Université de Paris, 91405 Orsay, France
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  • For correspondence: martin.crespi@ips2.universite-paris-saclay.fr

Published July 2020. DOI: https://doi.org/10.1104/pp.20.00446

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  • © 2020 American Society of Plant Biologists. All Rights Reserved.

Abstract

Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) 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 small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

  • Received April 15, 2020.
  • Accepted April 30, 2020.
  • Published May 13, 2020.
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Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
Thomas Blein, Coline Balzergue, Thomas Roulé, Marc Gabriel, Laetitia Scalisi, Tracy François, Céline Sorin, Aurélie Christ, Christian Godon, Etienne Delannoy, Marie-Laure Martin-Magniette, Laurent Nussaume, Caroline Hartmann, Daniel Gautheret, Thierry Desnos, Martin Crespi
Plant Physiology Jul 2020, 183 (3) 1058-1072; DOI: 10.1104/pp.20.00446

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Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
Thomas Blein, Coline Balzergue, Thomas Roulé, Marc Gabriel, Laetitia Scalisi, Tracy François, Céline Sorin, Aurélie Christ, Christian Godon, Etienne Delannoy, Marie-Laure Martin-Magniette, Laurent Nussaume, Caroline Hartmann, Daniel Gautheret, Thierry Desnos, Martin Crespi
Plant Physiology Jul 2020, 183 (3) 1058-1072; DOI: 10.1104/pp.20.00446
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Plant Physiology: 183 (3)
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