*4.2. Observations of Sepal Anatomy and Determination of Total Anthocyanin Content*

Spot and non-spot sepal tissue of full bud were cut into segments longitudinally (approx.10 mm × 5 mm), and the upper epidermis and dorsal epidermis were separated with forceps. The sections were observed and photographed with a light microscope (Primo Vert, Zeiss, Germany).

The total anthocyanin content of *Phalaenopsis* sepal in spot and non-spot areas were determined by the pH differential method [36].

#### *4.3. RNA Extraction, cDNA Library Construction, and mRNA Sequencing*

RNAs were extracted from spot and non-spot parts of sepals of full bud using the modified Trizol method [6]. Two biological replicates were used for spot sepal and non-spot sepal. A total of 4 RNA-seq libraries were constructed from these sepals. RNA-Seq libraries were constructed using the RNA Library Prep Kit for Illumina according to the manufacturer's instructions (NEB, Ipswich, MA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system. The mRNA libraries were sequenced on the Illumina HiSeq 2000 platform (Illumina, San Diego, CA, USA) based on sequencing by synthesis with 150 bp paired-end reads (Biomarker Technologies, Wuhan, China).
