Growth Protocol:	Rice (Oryza sativa L. cv. Nipponbare) was used for all physiological experiments. Hydroponic experiments were performed under controlled conditions (day/night temperature of 30/22°C and a 12 hr photoperiod, 200 µmol photons m-2 s-1), allowing 0.5 l of hydroponic solution per plant. The hydroponic solution consisted of a modified solution as described in (Secco et al., 2013a), containing 1.425 mM NH4NO3, 0.513 mM K2SO4, 0.998 mM CaCl2, 1.643 mM MgSO4, 0.075 µM (NH4)6Mo7O24, 0.25 mM NaSiO3, 0.009 mM MnCl2, 0.019 µM H3BO3, 0.155 µM CuSO4, 0.152 µM ZnSO4 and 0.125 mM EDTA-Fe, with or without 0.323 mM NaH2PO4, resulting in the +Pi and -Pi conditions. The pH of the solution was adjusted to 5.5 and the solution was renewed every 3 day.
Treatment Protocol:	Rice seeds were first pre-germinated in tap water for 2 days before being transferred into the hydroponic solution, containing 0.323 mM Pi (+Pi) for 2 weeks. Half of the seedlings were then transferred to a solution lacking Pi (0 mM Pi) for 21 days, before being re-supplemented with 0.323 mM Pi for up to 31 days, while the other half of the seedlings continuously remained in +Pi conditions (control). During the resupply experiment, half of the rice seedlings were left in Pi deficient media, to serve as control. After 24 days of Pi starvation, plants grown under Pi deficient conditions were supplemented with 0.03 mM Pi (1/10th of Pi sufficient Pi concentration) until the end of the experiment to prevent them from dying.
Extract Protocol:	The total RNA from the roots tissues was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer's instructions.
Library Construction Protocol:	For RNA-seq library synthesis, total RNA was first depleted of rRNA using the Ribo-Zero rRNA removal kit (Plant Leaf, and Plant Seed/Root kits, Epicentre, Madison, WI). To do so, 1 µg of total RNA from root samples was used as input for rRNA removal. Sequencing libraries were generated using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA).

Molecule Type:	rRNA- RNA
Library Source:
Library Layout:	SINGLE
Library Strand:	Forward
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 1000
Strand-Specific:	Specific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate