RNA-seq of Arabidopsis expressing citrus BBX28: leaves
The rosette leaves were harvested from at least eight independent 3-week-old transgenic Arabidopsis plants expressing citrus BBX28,  and the resulting  total RNA was first assessed with NanoPhotometer spectrophotometer (IMPLEN, USA) and RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, USA) to ensure the quality and integrity. Sequencing library was generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturers recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from 1.5 g of total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer5X. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse TranscriptaseRNase H. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 200-250 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 L USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37C for 15 min followed by 5 min at 95C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.