Fig. 5

Coffea caffeine synthases and Gardenia crocin biosynthesis dioxygenase arose through genus-specific tandem duplications. a Microsynteny between Coffea and Gardenia around the caffeine synthases of the former and the first dedicated gene in crocin biosynthesis in Gardenia, GjCCD4a. b Simplified phylogenies (pruned from the trees provided in Figs. S27-S28) depicting the evolution of caffeine and crocin biosynthetic genes in Gentianales. Purple branches indicate clades that are Gentianales-specific; green, Rubiaceae-specific; red, Coffea-specific. The gene IDs used for the phylogenetic trees of NMTs and CCD are the following: CcNMT2 (Cc02_g09350), CcNMT4b (Cc09_g07000), CcNMT4a (Cc09_g06990), CcMTL (Cc09_g06950), CcNMT3 (Cc09_g06960), CcXMT (Cc09_g06970), CcDXMT (Cc01_g00720), CcMXMT (Cc00_g24720), GjNMT2 (Gj9A1032T108), GjNMT4a (Gj1A458T26), GjNMT4b (Gj1X458T25), GjNMT4c (Gj1A458T28), SlCCD4a (Solyc08g075480.2.1), SlCCDb (Solyc08g075490.2.1), CcCCD4 (Cc08_g05610), GjCCD4a (Gj9A597T69), GjCCD4b (Gj9A597T68), GjCCD4c (Gj9A597T67), GjCCD4d (Gj9P597T6), GsCCD4 (Gs_scaff312_1.38), CrCCD4a (CRO_T140281), CrCCD4b (CRO_T140282), CrCCD4c (CRO_T140277), and CgCCD4 (cal_g006885.t1). Gene IDs for those with the biochemical activities in question are shown in red. Gardenia gene IDs are shown in orange. All other gene IDs are shown in black. For the collapsed tree branches in the pruned trees, species abbreviations are as follows: At, Arabidopsis thaliana; Vv, Vitis vinifera; Sl, Solanum lycopersicum; Gs, Gelsemium sempervirens; Cr, Catharanthus roseus; Cg, Calotropis gigantea; Cc, Coffea canephora; Gj, Gardenia jasminoides; Bd, Buddleja davidii