S4-2
Raw  reads were first subject to 3 adapter removal and quality filtering (Q >  17 and length >= 25 bp). Clean reads were mapped to the D. catenatum  genome sequence (http://herbalplant.ynau.edu.cn/) using TopHat. Read counts  of each gene were summarized by the HTSeq-count. Lowly expressed genes were  removed and only genes with an expression level of at least 1 RPM (readss per  million) in at least two samples were kept for further analysis.