*2.3. Transcriptome De Novo Assembly, Gene Functional Annotation, and Differentially Expressed Genes (DEGs) Analyses*

The raw reads of transcriptome sequencing were filtered using SOAPnuke v.15.2 (BIG, Shenzhen, China), and a set of clean reads was obtained. After de novo assembling, the clean reads were mapped to the pepper reference genome [36]. Genes were functionally annotated based on the NCBI non-redundant (Nr) [37], Gene Ontology (GO) [38], and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases [39]. For gene expression analysis, the numbers of matched reads were calculated and then normalized to RPKM by RSEM v.1.2.12. Significant differential expression genes (DEGs) were identified as those with a fold-change ≥ 2.0 and an FDR ≤ 0.001. DEGs were clustered using GO-Term Finder software, and pathway enrichment analysis was performed based on terms from the KEGG database.
