Transcriptome Sequencing Analysis

Ten-day-old seedlings were dehydrated on dry filter paper in petri dishes until loss of 40% fresh weight and then incubated for 2 h in sealed plastic bags to prevent further water loss. Total RNA was extracted using the RNeasy Mini Kit (Invitrogen), and DNA was cleaned by DNase I (New England Biolabs). About 2 to 4 µg of cleaned total RNA was used to construct RNA-seq libraries by using the Illumina Whole Transcriptome Analysis Kit following the standard protocol (Illumina HiSeq system) and sequenced on the HiSeq 2000 platform. The gene expression levels (fragments per kilobase of transcript per million mapped reads, FPKM) were calculated with Cufflinks (2.0.2) as described previously (Trapnell et al., 2010; Chen et al., 2013). Two biological replicates were performed.