Fig. 1: Somatic embryogenesis in V. vinifera is a stage-organized process that exhibits an hourglass-shaped phylogeny-ontogeny correlation.

a The sampled developmental stages of somatic embryogenesis in V. vinifera: early induction (EI), pre-globular stage (PG), globular stage 1 (G1), globular stage 2 (G2), heart stage (H), torpedo stage 1 (T1), torpedo stage 2 (T2), cotyledonary stage 1 (C1), cotyledonary stage 2 (C2), seedling (S), seedling with epicotyl (EP) and juvenile plant (JP). Scale bars: 0.5 mm (EI–C2), 2 mm (S), 3 mm (EP), 1 cm (JP). The somatic embryogenesis stages were determined following previously described morphological criteria⁴³. We performed transcriptome sequencing in n = 5 (C2 and EP stages) and n = 3 (the remaining 10 stages) biological replicates. For every sampled developmental stage, we showed corresponding hormones that were present in media as well as photoperiod at which developing plants were cultivated. “Long day” marks photoperiod of 18 h light and 6 h dark. For an easy reference, we also depicted post-induction time in weeks (w), global developmental phases, and expression phases derived from our correlation analysis. b Pearson’s correlation coefficients between somatic embryogenesis developmental stages in all-against-all comparison. Early (EI–G2), mid (H–T1), T2, C1, and late (C2–JP) expression stages are marked. c The transcriptome age index (TAI) of somatic embryogenesis shows an hourglass pattern. The heart stage of the mid-developmental period expresses the evolutionary oldest transcriptome, while earlier and later stages express evolutionary younger ones. We tested the significance of the TAI pattern using the flat-line test, while the gray shaded area represents ±1 standard deviation estimated using permutation analysis (see “Methods”). d The transcriptome nonsynonymous divergence index (TdNI) of somatic embryogenesis shows an hourglass pattern. The heart stage of the mid-developmental period expresses the most conserved genes at nonsynonymous divergence sites, while earlier and later stages express more diverged genes. Nonsynonymous divergence rates were estimated in V. vinifera–V. arizonica pairwise comparisons (see “Methods”). We tested the significance of the TdNI pattern using the flat-line test, while the gray shaded area represents ±1 standard deviation estimated using permutation analysis (see “Methods”). The corresponding transcriptome synonymous divergence index (TdSI) and transcriptome codon bias index (TCBI) profiles are shown in Supplementary Fig. 2e. e A schematic comparison between the TAI profile of V. vinifera somatic embryogenesis that we recovered in this study and the TAI profile of A. thaliana zygotic embryogenesis reported previously⁴. To make the hourglass patterns visually comparable between these studies, the TAI values were normalized to a range between 0 and 1 (see “Methods”).