*4.6. Small RNA Library Construction and Sequencing*

RNA was extracted from spot and non-spot sepal using the modified Trizol method [6], and 4 small RNA libraries from sepal spot and non-spot samples with 2 biological replicates were constructed and sequenced by SBQ500 sequencing method (BGI, Wuhan, China). Then the low-quality, 5 primer contaminants, without 3 primers and insert tags, and sequences fewer than 18 nucleotides (nt) were filtered out to obtain clean reads from raw data reads. The final clean reads of the 4 libraries were mapped to *Phalaenopsis* genome and other smallRNA databases using Bowtie2 [41]. All the remaining clean sequences were annotated into different classes to remove rRNA, scRNA, snoRNA, snRNA, and tRNA using miRBase, siRNA, piRNA, snoRNA database with Bowtie2 [42] and Rfam database with cmsearch [43]. The novel miRNAs were predicted by Mireap software (https://sourceforge.net/ projects/mireap/).
