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. 2025 Sep 22;26:807. doi: 10.1186/s12864-025-12061-3

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© The Author(s) 2025

Open Access This 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/.

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Fig. 4 — Schematic overview of different branches of the flavonoid and carotenoid biosynthesis and the detection via CoExpPhylo. Enzymes highlighted with a colored background were used as input baits for the analysis of the corresponding biosynthetic branch. Colored check marks indicate the Orthologous Coexpressed Groups (OCGs) retrieved for that branch. A Displayed enzymes are PHE ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3’-hydroxylase (F3’H), flavonoid 3’,5’-hydroxylase (F3′5’H), flavonol synthase (FLS), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductase (LAR), transparent testa 12 (TT12), anthocyanidin synthase/leucoanthocyanidin dioxygenase (ANS/LDOX), anthocyanidin reductase (ANR), anthocyanin-related glutathione S-transferase (arGST), UDP-dependent anthocyanidin-3-O-glycosyltransferase (3GT), O-methyltransferase (OMT). The dotted arrow indicates a transporter. B Venn diagram showing the overlap of genes identified in the three biosynthetic pathways: anthocyanins, proanthocyanidins and flavonols. C Displayed enzymes are phytoene synthase (PSY), phytoene desaturase (PDS), ζ-carotene desaturase (ZDS), carotenoid isomerase (CRTISO), ⁠lycopene β -cyclase (β-LCY), lycopene ε -cyclase (ε-LCY), lutein deficient5/cytochrome P450-family 97-A3 (LUT5/CYP97A3), lutein deficient1/cytochrome P450-family 97-C1 (LUT1/CYP97C1), beta carotenoid hydroxylase 1 (BCH1), and beta carotenoid hydroxylase 2 (BCH2)