Biomass composition.

Data collected from publications, and respective processing to include it in the GSM models. (XLSX)</p

Flux values for simulations obtained with pFBA and FVA under different environmental conditions using the different models.

Flux values for simulations obtained with pFBA and FVA under different environmental conditions using the different models.</p

General properties of the generic and tissue-specific GSM models. Genes were predicted based on the cork oak genome and then used to develop the GSM model.

Orphan reactions: reactions without gene association (excluding exchange reactions). The reactions were divided according with the respective metabolic role: metabolic (enzymatic and spontaneous) and transport, and the respective compartment. The number of genes, metabolites, and reactions were determined in the generic model and each tissue-specific model, generated with troppo.</p

Number of reactions in the iEC7871 not identified in the <i>A</i>. <i>thaliana</i> and <i>Z</i>. <i>mays</i> [18] models for each pathway (so-called unique reactions).

Only pathways with more than 20 unique reactions were included in this table. The complete table is available in Table H in S2 File. The KEGG pathways were organized according to the main areas of KEGG metabolism: 1- Xenobiotics biodegradation and metabolism; 2- Lipid metabolism; 3- Metabolism of cofactors and vitamins; 4- Amino acid metabolism and Metabolism of other amino acids; 5- Metabolism of terpenoids and polyketides; 6- Biosynthesis of other secondary metabolites; 7- Nucleotide metabolism; 8- Genetic Information Processing.</p

General properties (genes, reactions, metabolites, and compartments) of the <i>Q</i>. <i>suber</i> model, and other five published plant GSM models.

General properties (genes, reactions, metabolites, and compartments) of the Q. suber model, and other five published plant GSM models.</p

List of top ten enzymatic reaction targets ranked by the evaluation function for increased suberin production.

List of top ten enzymatic reaction targets ranked by the evaluation function for increased suberin production.</p

The biomass compositions of the leaf, inner bark, and phellogen were determined using data retrieved from published plant GSM models and available experimental data.

DNA, RNA, and cofactors were omitted from the plot as their contribution to the biomass is very low (S3 File.</p

Biosynthetic pathway of suberin, waxes, and lignin monomers.

Reactions not available at KEGG are highlighted in red. The components of suberin, lignin, and waxes are underlined. The C:16 and C:18 fatty acids produced in the plastid are transported to the endoplasmic reticulum, where they can be elongated and unsaturated, and follow the suberin monomer biosynthesis pathway. Cytochromes P450 (CYPs), peroxygenases, epoxy hydroxylases, ω-oxo-fatty acid dehydrogenases, and ω-hydroxy-fatty acid dehydrogenases catalyse successive reactions to produce the aliphatic monomers. Farnesyl diphosphate, produced from isopentenyl diphosphate provided by the cytosolic mevalonate (MVA) pathway or by the plastidic methylerythritol phosphate (EMP) pathway is used as the initial precursor of steroids in the ER. 2,3-Epoxysqualene is converted into sterols and terpenoids, monomers of the wax component of the phellogen. The phenylpropanoid pathway uses phenylalanine produced in the leaf’s chloroplasts, to produce cinnamate. The pathway follows in the cytosolic surface of the endoplasmic reticulum, and then in the cytosol, producing the lignin monomers. 4CL– 4-Coumarate CoA ligase, AMO: β-amyrin monooxygenase, C3H: p-coumarate 3-hydroxylase, C4H: cinnamate 4-hydroxylase, CAD: cinnamyl alcohol dehydrogenase, CCR: cinnamoyl-CoA reductase, COMT: Caffeoyl-CoA O-methyltransferase, EH: epoxide hydroxylase, FDFT: farnesyl diphosphate farnesyltransferase, FS: friedelin synthase, HFADH: ω-hydroxy-fatty acid dehydrogenase, LS—lupeol synthase, OFADH: ω-oxo-fatty acid dehydrogenase, PAL: phenylalanine ammonia-lyase, PO: peroxygenase, SQE: squalene monooxygenase. A. thaliana identifiers were used for the nomenclature of CYPs for convenience. The IDs of the reactions catalysed by these enzymes can be found in Table L in S2 File.</p

Metabolic map of carbon and nitrogen assimilation through photorespiration (Fig A).

Analysis of the quantum yield for different carboxylation/oxygenation ratio of Rubisco (Fig B). Summary of the simulations detailed in S4 File. (PDF)</p

Results of the genome annotation, and respective analysis.

Results of the genome annotation, and respective analysis.</p