The paired-end reads for protocorm, juvenile tuber, immature tuber, mature tuber, scape samples were mapped to the G. elata genome using TopHat. The total numbers of aligned reads were normalized by gene length and sequencing depth for an accurate estimation of expression level. We used these normalized read counts (RPKM) as the expression level for each gene. Then, DESeq was used to identify differentially expressed genes (Supplementary Tables 44-58). A repeated bisection method and a top–down hierarchical clustering algorithm in gCLUTO (http://glaros.dtc.umn.edu/gkhome/cluto/gcluto/overview) were used to generate the expression profiles of all differently expressed genes.