Transcriptome Analysis of Tibetan Herb

Samples of root, stem, leave, and fruit tissues from three individuals were collected for total RNA extraction. We extracted total RNA from each sample using the MiniBEST Plant RNA Extraction Kit (TaKaRa, China) following the manufacturer’s protocol. The cDNA was synthesized using RNA to cDNA EcoDry Premix (Clontech) with oligo (dT) primer. The paired-end library was constructed based on the Paired-End sample Preparation kit protocol (Illumina, USA). RNA sequencing was performed on the NextSeq 500 platform (Illumina, USA). For RNA-seq analysis, we first used the HISAT2 software package to map RNA-seq data of roots, stems, leaves, and fruits to the H. tibetana genome [61 (link)]. The RSEM software was used to calculate the gene expression level as fragments per kilobase per million (FPKM) [62 (link)]. We used DESeq2 to identify differential expression genes with an adjusted p-value ≤ 0.05.