Table 2.
Metabolic pathways with at least two genes that are differentially expressed when in planta conditions are compared with the temporally related axenic cultures and when early in vitro is compared with late in vitro.
| Pathway | Comparisons between in planta and in vitro at equivalent developmental stages | Comparisons between in vitro developmental stages | ||||||
|---|---|---|---|---|---|---|---|---|
| 3 dpi IP > 4 dpi IV | 3 dpi IP < 4 dpi IV | 5 dpi IP > 4 dpi IV | 5 dpi IP < 4 dpi IV | Late IP > 16 dpi IV | Late IP < 16 dpi IV | 4 dpi IV > 16 dpi IV | 4 dpi IV < 16 dpi IV | |
| 4‐Aminobutyrate degradation III (4 genes) | 2 | 1 | 3 | |||||
| Arginine biosynthesis II (acetyl cycle) (9 genes) | 4 | 4 | ||||||
| Chorismate biosynthesis (7 genes) | 1 | 2 | 1 | |||||
| Cyclopropane fatty acid (CFA) biosynthesis (2 genes) | 2 | |||||||
| Ergosterol biosynthesis (6 genes) | 2 | 1 | 1 | 1 | ||||
| Fatty acid biosynthesis—initial steps I (10 genes) | 2 | |||||||
| Fatty acid elongation—saturated (25 genes) | 5 | 7 | 6 | 1 | 9 | 1 | 4 | |
| Fatty acid β‐oxidation II (core pathway) (16 genes) | 2 | 2 | 1 | 1 | 3 | 2 | ||
| Fatty acid β‐oxidation IV (unsaturated, even number) (7 genes) | 2 | 1 | ||||||
| Folate polyglutamylation I (5 genes) | 2 | |||||||
| Folate transformations (8 genes) | 1 | 1 | 4 | |||||
| Gluconeogenesis (13 genes) | 2 | 2 | 1 | 1 | 1 | |||
| Glutamate biosynthesis III (2 genes) | 2 | 2 | 2 | |||||
| Homogalacturonan degradation (5 genes) | 2 | 1 | 2 | 1 | ||||
| Glycogen biosynthesis II (from UDP‐d‐glucose) (4 genes) | 1 | 1 | 2 | |||||
| Glycogen degradation II (5 genes) | 2 | 1 | 3 | 3 | 1 | |||
| Isoleucine biosynthesis from threonine (13 genes) | 4 | 3 | 1 | 2 | 3 | |||
| Isoleucine degradation I (14 genes) | 3 | 3 | 2 | 2 | 2 | |||
| l‐Arabinose degradation II (1 gene) | 1 | |||||||
| l‐Cysteine degradation I (6 genes) | 1 | 1 | 1 | |||||
| Leucine biosynthesis (10 genes) | 3 | 3 | 2 | 1 | ||||
| Leucine degradation I (13 genes) | 3 | 1 | 3 | 1 | 2 | 1 | ||
| l‐Serine degradation (2 genes) | 2 | 2 | ||||||
| Lysine biosynthesis IV (6 genes) | 2 | 1 | 2 | 3 | 1 | |||
| Melibiose degradation (4 genes) | 2 | 2 | 2 | |||||
| Methionine degradation I (to homocysteine) (4 genes) | 2 | 2 | 2 | |||||
| Nitrate reduction V (assimilatory) (7 genes) | 4 | 2 | 4 | |||||
| Ornithine biosynthesis (6 genes) | 2 | 3 | 3 | |||||
| Oxidative ethanol degradation I (22 genes) | 6 | 4 | 5 | 2 | 8 | 1 | 1 | 1 |
| Pantothenate biosynthesis I (10 genes) | 4 | 4 | 4 | 1 | 1 | |||
| Phenylalanine biosynthesis I (4 genes) | 1 | 2 | 2 | |||||
| Phospholipases (8 genes) | 3 | 1 | ||||||
| Proline biosynthesis I (7 genes) | 2 | 2 | 2 | |||||
| Purine nucleotides de novo biosynthesis II (11 genes) | 3 | 1 | 2 | 3 | ||||
| Pyruvate fermentation to ethanol II (17 genes) | 5 | 4 | 3 | 3 | 6 | 2 | 1 | 1 |
| Removal of superoxide radicals (9 genes) | 1 | 1 | 1 | 2 | 1 | |||
| S‐Adenosyl‐l‐methionine cycle (4 genes) | 2 | 2 | 3 | |||||
| Salvage pathways of adenine, hypoxanthine and their nucleosides (5 genes) | 2 | 2 | 1 | |||||
| Sorbitol utilization (5 genes) | 4 | 4 | 4 | 1 | ||||
| Spermidine biosynthesis (2 genes) | 2 | 1 | 1 | |||||
| β‐Alanine biosynthesis V (8 genes) | 1 | 1 | 2 | 2 | 1 | |||
| β‐Alanine degradation I (3 genes) | 2 | 1 | 2 | |||||
| Sucrose degradation to ethanol and lactate (anaerobic) (25 genes) | 5 | 6 | 3 | 4 | 6 | 3 | 3 | 1 |
| Sulphite oxidation IV (3 genes) | 1 | 1 | 2 | |||||
| Tetrapyrrole biosynthesis II (5 genes) | 1 | 2 | 1 | 1 | ||||
| Trehalose degradation II (trehalase) (5 genes) | 1 | 3 | 1 | 1 | 1 | |||
| Triacylglycerol biosynthesis (8 genes) | 1 | 3 | ||||||
| tRNA charging pathway (25 genes) | 2 | 1 | 1 | |||||
| Tryptophan degradation to 2‐amino‐3‐carboxymuconate semialdehyde (4 genes) | 2 | 1 | 1 | 2 | 1 | 2 | ||
| Tryptophan degradation VI (via tryptamine) (8 genes) | 5 | 1 | 3 | 1 | 3 | 1 | ||
| Tyrosine degradation I (7 genes) | 1 | 2 | 5 | 1 | ||||
| UDP‐N‐Acetyl‐d‐galactosamine biosynthesis II (4 genes) | 2 | 1 | ||||||
| Urate biosynthesis (5 genes) | 2 | 2 | 1 | |||||
| Valine biosynthesis (12 genes) | 4 | 3 | 1 | 2 | 3 | |||
| Valine degradation II (24 genes) | 5 | 7 | 3 | 6 | 6 | 4 | 2 | 1 |
| Xylitol degradation (4 genes) | 1 | 2 | 1 | 1 | ||||
UDP, uridine diphosphate.