title: ControlR3
design: Total RNA was extracted from tissues using a TaKaRaMiniBEST PlantRNA Extraction Kit. During total RNA extraction, genomic DNA was removed by the DNase I treatment.Then RNA was analyzed either using a ND-8000spectrophotometer (NanodropTechnologies, Inc., Wilmington, DE, USA) after purification, by agarose gelelectrophoresis, or using a2100-Bioanalyzer(AgilentTechnologies, Santa Clara, CA, USA) to determine the RNA quantity. Those RNA samples with no smear seen on agarose gels, a 260/280 ratio above 2.0, and a RNA integrity number greater than 8.0 were used.  For RNA-sequencing, RNA samples (three biological replicates per conditionand four plants per replicate) were then sent to Genergy Biotechnology Corporation (http://www.genenergy.cn/) for sequencing. Total RNA was first depleted of rRNA using the Ribo-Zero rRNA removal kit (Plant Leaf and Plant Seed/Root kits; Epicentre), namely, 1 μg of total RNA from root samples was used as input for rRNAremoval. Sequencing libraries were generated using the TruSeq RNA sample prep kit (Illumina). The libraries were sequenced as 151-bp paired-end reads using Illumina HiSeq X ten according to the manufacturer's instructions.