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

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.