Transcriptome Analysis of Plant Samples

The total RNA from each sample was extracted using a plant total RNA isolation kit (Tiangen, Beijing, China) based on the manufacturer’s instructions. A total of nine cDNA libraries (three replicates each of CK, LS and HS) were constructed. After estimating the quality, concentration and integrity of total RNA, the RNA was sequenced on the Illumina HiSeq platform (HiSeq^TM 2500, San Diego, CA, USA). To ensure the quality of the raw reads, they were filtered using Fastp [94 (link)] software (version 0.12) to obtain high-quality clean reads. De novo assembly of unigenes was performed using Trinity [29 (link)] software (v2.11.0). The longest transcript at each locus was considered a unigene, and the unigene IDs were automatically generated by the software. Gene functional annotation of the assembled unigenes was performed using public databases, including Nr [30 ], Swiss-Prot [31 (link)], GO [32 (link)], KOG [33 (link)], KEGG [34 (link)], Pfam [35 (link)] and Trembl databases.