Differentially-expressed genes that are involved in selected key metabolic pathways among three major cellular compartments. Genes involved in photosynthesis, glycolysis/gluconeogenesis, citrate cycle (TCA cycle), anaerobic respiration, glycolic acid oxidation, and fatty acid β-oxdidation pathways are shown. The enzymes (# denotes key or rate-limiting enzymes) are: E1#, fructose-1,6-bisphosphatase; E2, fructose-bisphosphate aldolase; E3, glyceraldehyde 3-phosphate dehydrogenase; E4, phosphoglycerate kinase; E5#, pyruvate kinase; E6#, alcohol dehydrogenase; E7, catalase; E8, acyl-CoA dehydrogenase; E9, succinyl-CoA ligase; E10, malate dehydrogenase; E11#, ribulose bisphosphate carboxylase; E12, transketolase; E13, ribulose-phosphate 3-epimerase; E14, phosphoribulokinase; E15, beta-phosphoglucomutase, 1,4-alpha-glucan branching enzyme; E16#, sucrose phosphate synthase; E17#, sucrose synthase. Proteins and enzymes in the light reaction complex are plastocyanin, ferredoxin [2Fe-2S], chlorophyll A-B binding protein, photosystem II protein PsbX, photosystem II protein PsbW, photosystem II protein PsbY, photosystem II oxygen evolving complex protein PsbP, photosystem II protein PsbR, photosystem II manganese-stabilizing protein PsbO, photosystem II oxygen evolving complex protein PsbQ, photosystem I reaction centre (subunit XI PsaL), photosystem I psaG/psaK protein, photosystem I reaction centre subunit N, photosystem I reaction center protein PsaF (subunit III), NADH:flavin oxidoreductase/NADH oxidase, and cytochrome b ubiquinol oxidase. The ratios of up- (+) or down (-) -regulated tags are indicated. Detailed information for light reaction complexes is listed in Additional file 6. Note that the key enzymes are either up- or down-regulated in three tissues; this behavior suggests active yet unique regulations in the hybrid.