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. 2020 Jun 18;18:63. doi: 10.1186/s12915-020-00795-3

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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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