Transcriptome expression divergence during meristem maturation and precocious gene expression in single-flowered species. Pairwise transcriptome distance measured by Euclidean distance between species and within stage showed elevated transcriptome expression divergence in the combined transitional stages (LVM and TM) for all 282 dynamic orthogroups (LVM/TM vs. MVM P < 0.026; LVM/TM vs. FM P < 0.012; Kolmogorov-Smirnov test) (A) and 63 dynamic transcription factor orthogroups (LVM/TM vs. MVM P < 0.038; LVM/TM vs. FM P < 0.065; Kolmogorov-Smirnov test) (B). K-means clustering of Z-score normalized tomato (Sl) dynamic genes (12 clusters) was performed. Orthologs from the single-flowered tobacco (Nb) and pepper (Ca) were then subclustered (10 subclusters) for each of the 12 tomato clusters. (C,D) Representative clusters and subclusters showing tomato FM-peaking (C) and TM-peaking (D) genes in tomato (red lines) compared to orthologs from single-flowered species (blue lines). Shown are orthogroups with conserved (Cons) expression (top), precocious expression peaking one stage early (middle), and precocious expression peaking in the same meristem stage as tomato (bottom). The number of genes (N) in each specific Cluster:Subcluster (C:S) is indicated above. Gene expression was compared on a gene-by-gene basis to more precisely identify precocious and conserved genes (Methods). (E,F) Venn diagrams showing overlap between tobacco and pepper precocious orthogroups from the floral (E) and transition (F) stages identified in the gene-by-gene analysis. A substantial proportion of orthogroups expressed precociously in both tobacco and pepper are transcription factors (50% and 23%, respectively). (G,H) Representative precocious floral (G) and transitional (H) orthogroups, scaled from 0 to 1, in tomato, pepper, tobacco, and S. peruvianum. Notably, precocious orthogroups include the known key floral identity F-box gene, ANANTHA, and the transition homeobox gene, COMPOUND INFLORESCENCE (Lippman et al. 2008).
