2.5 Differential gene expression and pathway analysis
To quantify the gene expression levels from the transcriptomes, we utilized Salmon tool (Patro et al., 2017), which was able to identify and quantify the known gene isoforms. Differentially expressed genes (DEGs) between the light treatments (red vs. control, blue vs. control) were identified using DESeq2 v3.10 software package (Love et al., 2014) with false discovery rate (FDR) adjusted p-value set to 0.05. Log2 fold change ratio between ≥ 2 and ≤ -2 was used to obtain the list of up- and down-regulated genes.
Gene Ontology (GO) terms for the transcripts were analyzed using GOseq v3.11 software (https://bioconductor.org/packages/release/bioc/html/goseq.html) in R-package followed by enrichment analysis using Fisher’s exact test. For validation and to improve the accuracy in GO determination, the top 500 differentially expressed genes from both the contrasts (red vs. control, blue vs. control) were extracted and annotated with Blast2GO suite (Gotz et al., 2008). KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis was performed in KOBAS v3.0 tool (Wu et al., 2006) followed by interpreting the KEGG Orthology terms (KO) in KAAS (KEGG Automated Annotation Server) using Vitis viniferaas a reference organism for obtaining the KO identifiers. The original figures and pathway representations were created withwww.biorender.com .