RNA-seq

Total RNA was extracted from rose petals as described in Wu et al. and Tian et al.^88,93, and genomic DNA contamination was removed using RNase-free DNase I (Promega). The quality and quantity of the RNA were assessed using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Samples with an RNA integrity number (RIN) > 8 were used for RNA-seq by Beijing Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). One microgram of total RNA per sample was used for cDNA library construction and Illumina sequencing, and RNA-seq data were processed, assembled, and annotated as previously described^94,95. Clean RNA-seq reads were aligned to the reference genome (Rosa chinensis cv. Old Blush, GenBank ID 8255808) and deposited in the NCBI BioProject database under the accession number PRJNA808873. Finally, differentially expressed genes (DEGs) were analyzed according to the parameters (fold change ≥ 2 or ≤0.5, q-value ≤ 0.05) and subjected to GO and KEGG enrichment analyses. The stage 0 and stage 2 microarray datasets were obtained from the rose transcriptome database (http://bioinfo.bti.cornell.edu/rose).