Extended Data Fig. 1. Natural retinal biosynthetic pathway from isoprenoid precursors in Fragilariopsis cylindrus.

Bar charts show RNA-seq gene expression of genes involved in putative biosynthetic pathway of all-trans-retinal in Fragilariopsis cylindrus including the cytosolic MEV and plastid DXP/MEP (grey box) during nine replicated experimental conditions (n = 3). Color scale represents absolute gene expression values (FPKM) on a relative scale per gene/gene copy. Gene expression barcharts for identified enzymes and isoenzymes are shown together with Joint Genome Institute (JGI) protein identifiers. Data are presented as mean values +/- s.d. To distinguish gene models belonging to divergent allelic pairs encoding for a single enzyme, they are labelled with suffixes (‘_1’ and ‘_2’). Chemical compounds are represented as circles (red) and enzymes are represented as rounded rectangles (light blue) together with their essential cofactors. Abbreviations: BCMO, β-carotene 15,15’-monooxygenase; CHYB, β-carotene 3-hydroxylase; DMAPP, dimethylallyl diphosphate; DMATT, dimethylallyltranstransferase; FAD, flavin adenine dinucleotide; Fe²⁺ , ferrous iron; FMN, flavin mononucleotide; FPKM, fragments per kilobase of exon per million mapped fragments; FPP, farnesyl diphosphate; FPPS, farnesyl diphosphate synthase; GGPP, geranylgeranyl diphosphate; GGPPS, geranylgeranyl diphosphate synthase; GPP, geranyl diphosphate; IDI, IPP:DMAPP isomerase; IPP, isopentenyl diphosphate; LCYB, lycopene β-cyclase; MEP, Methylerythritol phosphate; MEV, mevalonic acid; Mg²⁺ , divalent magnesium ion; Mn²⁺ , divalent manganese ion; PDS, phytoene desaturase; PSY, phytoene synthase; ZDS, ζ-carotene desaturase; Z-ISO, ζ-carotene isomerase.

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