Landscape of the non-coding 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 M. Desnos, Martin Crespi

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Root 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.
Original languageEnglish (US)
Pages (from-to)pp.00446.2020
JournalPlant Physiology
StatePublished - May 13 2020
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): CRG4, OCRF-2014-CRG
Acknowledgements: This 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).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.


Dive into the research topics of 'Landscape of the non-coding transcriptome response of two Arabidopsis ecotypes to phosphate starvation'. Together they form a unique fingerprint.

Cite this