Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery

David Secco, M. Jabnoune, Hayden Walker, H. Shou, P. Wu, Y. Poirier, James Whelan

Research output: Contribution to journalArticle

129 Citations (Scopus)

Abstract

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation-induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants. © 2013 American Society of Plant Biologists. All rights reserved.
Original languageEnglish
Pages (from-to)4285-4304
JournalPlant Cell
Volume25
Issue number11
DOIs
Publication statusPublished - 2013

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Starvation
starvation
Phosphates
phosphates
rice
shoots
homeostasis
Homeostasis
Gene Expression Profiling
MicroRNAs
transcriptomics
microRNA
Protein Isoforms
Spatio-Temporal Analysis
RNA Sequence Analysis
DNA libraries
crop models
translation (genetics)
Genes
biologists

Cite this

Secco, David ; Jabnoune, M. ; Walker, Hayden ; Shou, H. ; Wu, P. ; Poirier, Y. ; Whelan, James. / Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. In: Plant Cell. 2013 ; Vol. 25, No. 11. pp. 4285-4304.
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abstract = "Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled. A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several genes also showed induction of unannotated splice isoforms under Pi starvation. Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation-induced isoform, which was associated with increased translation activity. In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250. In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plants. {\circledC} 2013 American Society of Plant Biologists. All rights reserved.",
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Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. / Secco, David; Jabnoune, M.; Walker, Hayden; Shou, H.; Wu, P.; Poirier, Y.; Whelan, James.

In: Plant Cell, Vol. 25, No. 11, 2013, p. 4285-4304.

Research output: Contribution to journalArticle

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