Table 2.
KEGG pathways of DEGs.
| 2A. KEGG pathways of DEGs in CK-L vs. D-L | ||||
| # | Pathway | Annotation (713) | p-Value | Pathway ID |
| 1 | Metabolic pathways | 210 (29.45%) | 1.487446e-06 | ko01100 |
| 2 | Biosynthesis of secondary metabolites | 133 (18.65%) | 2.375184e-06 | ko01110 |
| 3 | Pyruvate metabolism | 20 (2.81%) | 0.0003487765 | ko00620 |
| 4 | Arginine and proline metabolism | 13 (1.82%) | 0.001129843 | ko00330 |
| 5 | Glycine, serine and threonine metabolism | 16 (2.24%) | 0.001321938 | ko00260 |
| 6 | Glutathione metabolism | 13 (1.82%) | 0.001345293 | ko00480 |
| 7 | Fatty acid degradation | 10 (1.4%) | 0.001462133 | ko00071 |
| 8 | Glycerolipid metabolism | 20 (2.81%) | 0.001519717 | ko00561 |
| 9 | Indole alkaloid biosynthesis | 6 (0.84%) | 0.001620922 | ko00901 |
| 10 | Regulation of autophagy | 13 (1.82%) | 0.001845656 | ko04140 |
| 11 | Ribosome | 37 (5.19%) | 0.002576793 | ko03010 |
| 12 | Tryptophan metabolism | 12 (1.68%) | 0.003130347 | ko00380 |
| 13 | Caffeine metabolism | 2 (0.28%) | 0.003729469 | ko00232 |
| 14 | Ascorbate and aldarate metabolism | 12 (1.68%) | 0.004263276 | ko00053 |
| 15 | Histidine metabolism | 7 (0.98%) | 0.004263308 | ko00340 |
| 16 | mRNA surveillance pathway | 27 (3.79%) | 0.005933953 | ko03015 |
| 17 | alpha-Linolenic acid metabolism | 9 (1.26%) | 0.007378807 | ko00592 |
| 18 | Ubiquinone and other terpenoid-quinone biosynthesis | 9 (1.26%) | 0.008113964 | ko00130 |
| 19 | Cysteine and methionine metabolism | 15 (2.1%) | 0.01011539 | ko00270 |
| 20 | Steroid biosynthesis | 7 (0.98%) | 0.01100777 | ko00100 |
| 21 | Pentose and glucuronate interconversions | 20 (2.81%) | 0.01620864 | ko00040 |
| 22 | Lysine degradation | 8 (1.12%) | 0.01643623 | ko00310 |
| 23 | Galactose metabolism | 13 (1.82%) | 0.019456 | ko00052 |
| 24 | Carotenoid biosynthesis | 8 (1.12%) | 0.0198106 | ko00906 |
| 2B. KEGG pathways of DEGs in CK-R vs. D-R | ||||
| # | Pathway | Annotation (3034) | p-Value | Pathway ID |
| 1 | Metabolic pathways | 926 (30.52%) | 1.348677e-29 | ko01100 |
| 2 | Biosynthesis of secondary metabolites | 570 (18.79%) | 2.264539e-23 | ko01110 |
| 3 | Photosynthesis–antenna proteins | 26 (0.86%) | 1.749018e-15 | ko00196 |
| 4 | Phenylpropanoid biosynthesis | 132 (4.35%) | 6.312239e-15 | ko00940 |
| 5 | Glycolysis/Gluconeogenesis | 105 (3.46%) | 9.470061e-12 | ko00010 |
| 6 | Carbon metabolism | 151 (4.98%) | 1.339665e-11 | ko01200 |
| 7 | Pyruvate metabolism | 70 (2.31%) | 7.136255e-08 | ko00620 |
| 8 | Carbon fixation in photosynthetic organisms | 60 (1.98%) | 1.608047e-07 | ko00710 |
| 9 | Photosynthesis | 37 (1.22%) | 4.541068e-07 | ko00195 |
| 10 | Plant hormone signal transduction | 172 (5.67%) | 6.098387e-07 | ko04075 |
| 11 | Arginine and proline metabolism | 43 (1.42%) | 3.276459e-06 | ko00330 |
| 12 | Circadian rhythm–plant | 66 (2.18%) | 4.310124e-06 | ko04712 |
| 13 | Nitrogen metabolism | 35 (1.15%) | 2.766522e-05 | ko00910 |
| 14 | Alanine, aspartate and glutamate metabolism | 43 (1.42%) | 3.614134e-05 | ko00250 |
| 15 | Sulfur metabolism | 25 (0.82%) | 0.0001004235 | ko00920 |
| 16 | Valine, leucine and isoleucine degradation | 32 (1.05%) | 0.0001541904 | ko00280 |
| 17 | Fructose and mannose metabolism | 44 (1.45%) | 0.0002872131 | ko00051 |
| 18 | Glycine, serine and threonine metabolism | 46 (1.52%) | 0.001046218 | ko00260 |
| 19 | Inositol phosphate metabolism | 34 (1.12%) | 0.001077126 | ko00562 |
| 20 | Stilbenoid, diarylheptanoid and gingerol biosynthesis | 45 (1.48%) | 0.001329768 | ko00945 |
| 21 | Biosynthesis of unsaturated fatty acids | 19 (0.63%) | 0.001333774 | ko01040 |
| 22 | Galactose metabolism | 45 (1.48%) | 0.002157363 | ko00052 |
| 23 | Starch and sucrose metabolism | 131 (4.32%) | 0.002175542 | ko00500 |
| 24 | Flavonoid biosynthesis | 31 (1.02%) | 0.002204898 | ko00941 |
| 25 | Taurine and hypotaurine metabolism | 14 (0.46%) | 0.002282244 | ko00430 |
| 26 | Zeatin biosynthesis | 18 (0.59%) | 0.003346513 | ko00908 |
| 27 | Citrate cycle (TCA cycle) | 33 (1.09%) | 0.00335235 | ko00020 |
| 28 | Diterpenoid biosynthesis | 25 (0.82%) | 0.003665961 | ko00904 |
| 29 | Pentose phosphate pathway | 44 (1.45%) | 0.004369615 | ko00030 |
| 30 | Biosynthesis of amino acids | 113 (3.72%) | 0.004736771 | ko01230 |
| 31 | beta-Alanine metabolism | 27 (0.89%) | 0.005233566 | ko00410 |
| 32 | Flavone and flavonol biosynthesis | 16 (0.53%) | 0.006075288 | ko00944 |
| 33 | Limonene and pinene degradation | 40 (1.32%) | 0.009214323 | ko00903 |
| 34 | Tyrosine metabolism | 25 (0.82%) | 0.01085029 | ko00350 |
| 35 | Glyoxylate and dicarboxylate metabolism | 44 (1.45%) | 0.01298711 | ko00630 |
| 36 | Amino sugar and nucleotide sugar metabolism | 60 (1.98%) | 0.0143173 | ko00520 |
| 37 | Cysteine and methionine metabolism | 45 (1.48%) | 0.0158524 | ko00270 |
| 38 | Ether lipid metabolism | 17 (0.56%) | 0.01740316 | ko00565 |
| 39 | Glucosinolate biosynthesis | 15 (0.49%) | 0.01936801 | ko00966 |
| 2C. KEGG pathways of DEGs in CK-L vs. S-L | ||||
| # | Pathway | Annotation (79) | p-Value | Pathway ID |
| 1 | ABC transporters | 5 (6.33%) | 0.0003552804 | ko02010 |
| 2 | Cutin, suberin, and wax biosynthesis | 3 (3.8%) | 0.01149507 | ko00073 |
| 3 | Regulation of autophagy | 3 (3.8%) | 0.01838196 | ko04140 |
| 2D. KEGG pathways of DEGs in CK-R vs. S-R | ||||
| # | Pathway | Annotation (502) | p-Value | Pathway ID |
| 1 | Nitrogen metabolism | 20 (3.98%) | 8.034565e-12 | ko00910 |
| 2 | Endocytosis | 38 (7.57%) | 9.001716e-06 | ko04144 |
| 3 | Phenylpropanoid biosynthesis | 26 (5.18%) | 3.331352e-05 | ko00940 |
| 4 | Ether lipid metabolism | 8 (1.59%) | 0.0002257619 | ko00565 |
| 5 | Glucosinolate biosynthesis | 7 (1.39%) | 0.0004888917 | ko00966 |
| 6 | Biosynthesis of secondary metabolites | 89 (17.73%) | 0.0005704914 | ko01110 |
| 7 | Plant-pathogen interaction | 40 (7.97%) | 0.004413053 | ko04626 |
| 8 | Metabolic pathways | 135 (26.89%) | 0.004841477 | ko01100 |
| 9 | ABC transporters | 10 (1.99%) | 0.005615396 | ko02010 |
| 10 | Arginine and proline metabolism | 9 (1.79%) | 0.006949714 | ko00330 |
| 11 | Flavonoid biosynthesis | 8 (1.59%) | 0.010255 | ko00941 |
| 12 | Indole alkaloid biosynthesis | 4 (0.8%) | 0.01178287 | ko00901 |
| 13 | Protein processing in endoplasmic reticulum | 24 (4.78%) | 0.01324247 | ko04141 |
| 14 | Plant hormone signal transduction | 30 (5.98%) | 0.01431411 | ko04075 |
| 15 | Pyruvate metabolism | 12 (2.39%) | 0.01621669 | ko00620 |
| 16 | Tryptophan metabolism | 8 (1.59%) | 0.01940078 | ko00380 |
The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed using DEGs from four treatment groups. CK-L (CK, leaves) vs. D-L (drought, leaves), CK-R (CK, roots) vs. D-R (drought, roots), CK-L vs. S-L (salinity, leaves), CK-R vs. S-R (salinity, roots) represent DEGs under these two abiotic stresses. Bolded rows represent the most highly enriched metabolic pathways.