## 2 Materials and Methods
### RNA-Seq Library Construction and Sequencing  
Total RNA of the samples was extracted via the modified CTAB (Bio Basic, Toronto, ON, Canada) method using an Optimal Dual-mode mRNA Library Prep Kit (BGI, Shezhen, China). The appropriate amount of tissue was ground into powder under liquid nitrogen and transferred to 1.5 mL of preheated CTAB lysis reagent (add 2% \(\beta\)-mercaptoethanol) at 65 \({}^{\circ}\)C, and incubated at 65 \({}^{\circ}\)C for 15 min. After incubation, the tube was cooled to room temperature, then centrifuged at 4 \({}^{\circ}\)C with 12,000\(\times\)\(g\) for 5 min. The supernatant was transferred into a 2.0 mL EP tube. A total of 200 \(\upmu\)L of chloroform/isoamyl alcohol (24:1) per mile littler of CTAB lysis buffer was added. The mixture was vortexed to mix and centrifuged at 4 \({}^{\circ}\)C with 12,000\(\times\)\(g\) for 10 min. Next, the clear upper aqueous layer was transferred to a 2.0 mL EP tube. An equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) was added. The mixture was vortexed to mix and centrifuged at 4 \({}^{\circ}\)C with 12,000\(\times\)\(g\) for 10 min. Then, the clear upper aqueous layer was transferred to a 2.0 mL EP tube. An equal volume of chloroform/isoamyl alcohol (24:1) was added. The mixture was vortexed to mix and centrifuged at 4 \({}^{\circ}\)C with 12,000\(\times\)\(g\) for 10 min. The final clear upper aqueous layer was transferred to a new 1.5 mL EP tube and added with 2/3 the aqueous layer's volume of isopropanol. The mixture was gently inverted to mix well and placed at \(-\)20 \({}^{\circ}\)C for 2 h. The RNA precipitation was collected through centrifugation at 4 \({}^{\circ}\)C with 12,000\(\times\)\(g\) for 20 min. The supernatant was removed, and the precipitation was resuspended and washed with 1 mL of 75% ethanol. After washing, the precipitation was centrifuged again at 4 \({}^{\circ}\)C with 17,500\(\times\)\(g\) for 3 min. The supernatant was discarded, and the precipitation was dried in the biosafety cabinet for 3-5 min. Finally, 20\(\upmu\)L-200\(\upmu\)L of DEPC-treated or RNase-free water was added to dissolve the RNA. Total RNA was treated using a mRNA enrichment method [7]. The mRNA enrichment: mRNA with polyA tail was enriched with magnetic beads with OligodT and a Oligitex mRNA kit. rRNA removal: RNA was hybridized with a DNA probe, RNaseH was selectively digested the DNA/RNA hybrid strand, the DNA probe was digested with DNaseI, then the desired RNA was purified. The RNA obtained was fragmented by interrupting the buffer, random N6 primers were reverse transcribed, and the two-stranded cDNA was synthesized to form double-stranded DNA. The ends of the synthesized double-stranded DNA were flattened and phosphorylated at the 5' end, forming a sticky end with an \"A\" at the 3' end and connecting a bubbling junction with a protruding \"T\" at the 3' end. The ligation products were PCR amplified by specific primers. The PCR product was thermally denatured into a single strand, and then a bridge primer was used to circulate the single-stranded DNA to obtain a single-stranded circular DNA library. AMPure XP beads were used to screen the cDNAs (\(\sim\)150 bp) before constructing the cDNA library. An RNA Library Prep Kit for Illumina1 (NEBNext1 UltraTM) was used to create sequencing libraries (NEB, Ipswich, MA, USA). cDNA libraries were constructed using the Illumina HiSeq(tm) X-Ten platform (BGI, Shenzhen, China). The constructed libraries were inspected by Agilent 2100 Bioanalyzer and Abisteponeplus Real-Time CrAnalyzer, and sequence ed after being qualified. Nine cDNA libraries of _R. chrysanthum_ in this experiment were produced by the Illumina HiSeq(tm) X-Ten platform based on the Shenzhen Huada Gene Science and Technology Research Co. (Shenzhen, China). The total raw reads of the nine samples ranged from 43.69 to 45.44 MB, and the Q20 was not less than 97.44%, indicating good sequencing quality. After data filtering, the total number of clean reads ranged from 42.21 to 43.51 MB.