*4.7. Expression Profile and RT-qPCR*

To compare color-related unigenes expression divergence, they were first normalized to RPKM (reads per kb per million reads). After that, different sample ratios of RPKM values were calculated. The FDR (false discovery rate) value was used to identify the threshold of the *p*-value in multiple tests in order to compute the significance of the differences among unigenes. Here, only FDR significance scores < 0.05, and log2 ratios > 1 were regarded as differentially expressed genes and used in subsequent analysis. In order to validate the expression pattern of the RNA-Seq results, ten important different expression genes (the primers used are listed in Table S1) were selected and measured using RT-qPCR on a Quant Studio 5 Real-Time PCR System (Thermo Fisher, Foster City, CA, USA) using the PowerUpTM SYBRTM Green Master Mix (Thermo Fisher, Foster City, CA, USA), according to the manufacturer's instructions. *PlUBC34* and *PlUBC3*5 (ubiquitin-conjugating enzyme; primers are also listed in Table S1) actin genes from *Pleione* were used as the internal control for the normalization of gene expression. Each sample (including three biological repetitions) was quantified in triplicate.
