Fig. 4: Standardized expression profiles of selected V. vinifera genes along somatic embryogenesis.

a Standardized expression profiles of genes annotated with GO term “Somatic embryogenesis” (GO:0010262) that showed an enrichment signal in Fig. 3 (EI stage). b Selected genes that have an important role in the induction of somatic embryogenesis according to the literature. c Three representative genes (DME, DRM2, and MET1) annotated with GO term “Epigenetic regulation of gene expression” (GO:0040029). This GO term showed an enrichment signal in Fig. 3 (EI and H stages). VAL1 is described in the literature to be important for chromatin modification. d Two representative genes (PRX73, WRKY40) annotated with GO term “Response to stress” (GO:0006950). This GO term showed enrichment signals in Fig. 3 (G1, G2, H, T1, and C1 stages). e Two representative genes (ABI3, ACC1) annotated with GO terms “Embryo development” (GO:0009790), “Multicellular organism development” (GO:0007275) and “Anatomical structure development” (GO:0048856). These GO terms showed enrichment signals in Fig. 3 (H stage). f Four representative genes (LHCA2, LHCA3, LHCA4, PGR5) annotated with GO terms “Plastid” (GO:0009536), “ Chloroplast” (GO:0009507), “Response to light stimulus” (GO:0009416), “Photosynthesis” (GO:0015979) and “Thylakoid” (GO:0009579). These GO terms showed enrichment signals in late developmental stages (C2, S, EP, and JP) in Fig. 3. Differential expressions along SE were tested by LRT test as implemented in DESeq2⁹¹. Resulting p values corrected by FDR are shown for every gene. Standardized expression value of 0 (black horizontal line) represents the median of expression levels for a respective gene. Gene names were obtained by searching for V. vinifera–A. thaliana orthologs in TAIR database⁹⁵. Correspondence between V. vinifera and A. thaliana genes together with standardized gene expression values can be found in Supplementary Data 4, and standardized gene expression profiles in Supplementary Data 9.