Table 1.
SuperFifty and paraquat alter the expression of genes representing fundamental biochemical pathways and physiological processes. Values are TMM (trimmed mean of M-values) values averaged across three biological replicates.
| Average TMM Values | Annotation | |||||
|---|---|---|---|---|---|---|
| Gene ID | H2O + H2O | H2O + PQ | SF + H2O | SF + PQ | Gene Name | Description/Function |
| ROS Inducible/Marker genes | ||||||
| AT2G21640 | 19.63 | 97.21 | 16.99 | 20.09 | Marker for oxidative stress response protein | |
| AT2G43510 | 64.24 | 214.79 | 40.04 | 47.11 | TI1 | Trypsin inhibitor, ROS marker |
| AT1G57630 | 4.07 | 76.13 | 4.36 | 4.51 | Toll-Interleukin-Resistance (TIR) domain family protein | |
| AT1G19020 | 36.57 | 247.44 | 26.24 | 33.40 | CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase, ROS marker | |
| AT1G05340 | 8.55 | 83.32 | 6.72 | 5.41 | Cysteine-rich stress protein, ROS marker | |
| ROS-Dependent PCD and Senescence | ||||||
| AT4G25110 | 1.75 | 6.47 | 2.07 | 2.99 | MC2 | Metacaspase 2 |
| AT1G16420 | 0.15 | 5.83 | 0.37 | 0.47 | MC8 | Metacaspase 8 |
| AT5G02190 | 2.78 | 2.35 | 7.33 | 8.40 | PSC1 | Promotion of cell survival 1 |
| AT5G02760 | 11.95 | 3.34 | 24.69 | 16.34 | SSPP | Senescence-suppressed protein phosphatase |
| AT4G27410 | 73.77 | 100.20 | 27.15 | 22.12 | RD26 | NAC (No Apical Meristem) domain transcriptional regulator superfamily protein |
| AT2G29350 | 31.09 | 395.89 | 19.27 | 16.05 | SAG13 | Senescence-associated gene 13 |
| ROS Detoxification | ||||||
| AT4G25100 | 459.32 | 277.99 | 664.81 | 715.19 | FSD1 | Fe superoxide dismutase 1 |
| AT4G09010 | 378.15 | 197.56 | 405.53 | 403.35 | APX4 | Ascorbate peroxidase 4 |
| AT5G57345 | 207.99 | 168.40 | 323.34 | 337.82 | OXR | Transmembrane OXR protein |
| AT4G39800 | 90.77 | 59.99 | 143.09 | 125.49 | MIPS1 | Myo-inositol-1-phosphate synthase 1 |
| AT5G21100 | 23.74 | 13.69 | 30.65 | 24.71 | AO | Plant L-ascorbate oxidase |
| AT5G51720 | 90.38 | 74.87 | 122.85 | 149.99 | NEET | 2 iron, 2 sulfur cluster binding protein |
| AT2G45560 | 43.67 | 26.91 | 67.23 | 67.88 | CYP76C1 | Cytochrome P450 family 76C, polypeptide 1 |
| AT2G46660 | 1.07 | 1.12 | 2.12 | 2.39 | CYP78A6 | Cytochrome P450, family 78A, polypeptide 6 |
| AT3G26310 | 7.03 | 4.62 | 11.01 | 9.27 | CYP71B35 | Cytochrome P450, family 71B, polypeptide35 |
| AT4G12320 | 32.62 | 28.68 | 66.06 | 74.88 | CYP706A6 | Cytochrome P450, family 706A, polypeptide6 |
| Photosynthesis | ||||||
| AT5G38420 | 1223.01 | 567.26 | 1376.75 | 1518.00 | RBCS2B | RuBisCO small chain |
| AT3G27690 | 799.90 | 303.31 | 1142.16 | 1032.88 | LHCB2.3 | Photosystem II LHC protein 2.3 |
| AT1G51400 | 1851.61 | 886.74 | 2086.64 | 2069.37 | Photosystem II 5 kD protein | |
| AT3G08940 | 3027.19 | 1449.15 | 3533.29 | 3026.97 | LHCB4.2 | Light harvesting complex photosystem II |
| AT3G63160 | 2922.20 | 1632.49 | 3304.18 | 3817.24 | OEP6 | Outer envelope membrane protein |
| AT3G27690 | 799.9 | 303.31 | 1142.16 | 1032.88 | LHCB2.4 | Chlorophyll a-b binding protein 2.4 |
| AT2G34430 | 3293.32 | 1182.9 | 3677.36 | 2958.81 | LHB1B1 | Light harvesting chlorophyll protein complex II subunit B1 |
| AT3G08940 | 3027.19 | 1449.15 | 3533.29 | 3026.97 | LHCB4.2 | Chlorophyll a-b binding protein CP29.2 |
| AT1G51400 | 1851.61 | 886.74 | 2086.64 | 2069.37 | Photosystem II 5kD protein | |
| AT2G34430 | 187.98 | 155.10 | 290.55 | 340.92 | LHB1B1 | LHC II subunit B1 |
| AT2G23670 | 187.98 | 155.10 | 290.55 | 340.92 | YCF37 | |
| AT1G03630 | 183.08 | 99.92 | 212.62 | 230.60 | PORC | Protochlorophyllide oxidoreductase C |
| Carbohydrate Metabolism and Cellulose Synthesis | ||||||
| AT1G64390 | 59.50 | 35.02 | 96.35 | 99.01 | Glycosyl hydrolase 9C2 | |
| AT2G01290 | 13.39 | 18.80 | 28.15 | 33.23 | Ribose-5-phosphate isomerase 2 | |
| AT1G70230 | 8.11 | 9.73 | 16.53 | 15.36 | Trichome Birefringence-Like 27 | |
| AT1G09350 | 24.01 | 8.36 | 45.35 | 36.17 | Galactinol synthase 3 | |
| Growth and Hormone Signaling | ||||||
| AT1G21310 | 32.88 | 197.79 | 33.87 | 31.90 | EXT3 | Extensin 3 |
| AT1G76930 | 73.22 | 149.21 | 53.68 | 60.34 | EXT4 | Extensin 4 |
| AT1G20190 | 59.51 | 26.15 | 93.85 | 83.53 | EXPA11 | Expansin 11 |
| AT2G20750 | 7.22 | 3.03 | 14.97 | 15.91 | EXPB1 | Expansin B1 |
| AT2G40610 | 50.54 | 18.78 | 99.07 | 79.61 | EXPA8 | Expansin A8 |
| AT5G57560 | 77.60 | 111.40 | 28.68 | 21.14 | TCH4 | Xyloglucan endotransglucosylase/hydrolase |
| AT2G14620 | 1.10 | 9.39 | 0.72 | 0.99 | XTH10 | Xyloglucan endotransglucosylase/hydrolase 10 |
| AT3G44990 | 29.15 | 26.58 | 73.92 | 99.89 | XTH31 | Xyloglucan endo-transglycosylase-related 8 |
| AT2G21210 | 25.55 | 15.99 | 53.74 | 65.71 | SAUR6 | SAUR-like auxin-responsive protein family |
| AT4G38860 | 27.84 | 11.74 | 56.72 | 52.80 | SAUR16 | SAUR-like auxin-responsive protein family |
| AT1G75580 | 4.29 | 4.93 | 8.13 | 10.95 | SAUR51 | SAUR-like auxin-responsive protein family |
| AT4G38840 | 97.43 | 43.53 | 134.62 | 150.76 | SAUR14 | SAUR-like auxin-responsive protein family |
| AT4G38850 | 9.36 | 3.92 | 15.98 | 15.53 | SAUR15 | SAUR-like auxin-responsive protein family |
| AT3G53250 | 1.95 | 0.68 | 4.90 | 3.47 | SAUR57 | SAUR-like auxin-responsive protein family |
| AT1G23080 | 65.86 | 32.20 | 94.83 | 82.05 | PIN7 | Auxin efflux carrier family protein |
| AT2G46870 | 4.70 | 3.63 | 9.38 | 8.47 | AP2/B3-like TF, auxin response. | |
| AT5G13320 | 3.71 | 16.08 | 2.97 | 3.60 | PBS3 | Auxin-responsive GH3 family protein |
| AT4G12550 | 4.01 | 1.69 | 5.66 | 6.45 | AIR1 | Auxin-Induced in Root cultures 1 |
| AT1G52830 | 4.59 | 1.53 | 6.79 | 4.16 | IAA6 | Indole-3-acetic acid 6 |
| AT1G74670 | 150.45 | 33.60 | 188.25 | 141.53 | GASA6 | Gibberellin-regulated family protein |
| AT1G02400 | 7.18 | 18.48 | 5.67 | 5.18 | GA2OX6 | Gibberellin 2-oxidase 6 (inactivates gibberellin) |
| AT1G15550 | 8.09 | 2.49 | 5.96 | 6.32 | GA3OX1 | Gibberellin 3-oxidase 1 |
| Autophagy | ||||||
| AT2G38470 | 48.75 | 142.40 | 26.84 | 36.51 | WRKY33 | WRKY DNA-binding protein 33 |
| AT2G45170 | 82.62 | 98.94 | 38.58 | 32.66 | ATG8E | AUTOPHAGY 8E |
| AT3G06420 | 18.68 | 35.54 | 14.28 | 14.12 | ATG8H | AUTOPHAGY 8H |
| Lipid Metabolism | ||||||
| AT1G19020 | 36.57 | 247.44 | 26.24 | 33.40 | CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase | |
| AT4G34200 | 75.62 | 216.87 | 76.14 | 74.59 | EDA9 | D-3-phosphoglycerate dehydrogenase |
| AT4G39670 | 3.43 | 50.87 | 2.08 | 2.82 | Glycolipid transfer protein (GLTP) family protein | |
| AT1G67800 | 10.05 | 23.91 | 10.77 | 12.32 | Copine (Calcium-dependent phospholipid-binding protein) family | |
| AT3G55470 | 18.33 | 57.91 | 20.04 | 21.00 | Ca-dependent lipid-binding (CaLB domain) | |
| AT5G14180 | 1.77 | 5.23 | 0.84 | 0.62 | MPL1 | Myzus persicae-induced lipase 1 |
| AT2G26560 | 45.59 | 364.62 | 38.48 | 42.54 | PLA2A | Phospholipase A 2A |
| AT1G13930 | 2740.50 | 1898.62 | 4318.3 | 3952.83 | Oleosin-B3 like protein | |
| AT1G51080 | 18.67 | 11.26 | 25.10 | 27.68 | Golgin family A proteins | |
| AT1G25054 | 0.61 | 0.57 | 6.08 | 3.07 | LPXC3, LPXC4 | UDP-3-O-acyl N-acetylglycosamine deacetylase |
| Transcription Factors and Stress-Related Genes | ||||||
| AT1G59930 | 4.7 | 2.6 | 8.94 | 10.58 | MADS-box transcription factor | |
| AT1G70890 | 136.76 | 85.38 | 171.01 | 170.27 | MLP43 | MLP-like protein 43 |
| AT1G75690 | 184.17 | 98.65 | 215.40 | 223.10 | DnaJ/Hsp40 | |
| AT1G78070 | 43.04 | 33.13 | 77.16 | 73.50 | Transducin/WD40 | |
| AT2G28720 | 95.98 | 74.93 | 131.89 | 151.73 | HTB3 | Histone super family protein |
| AT2G41090 | 300.65 | 461.43 | 464.31 | 652.82 | CML10 | Calcium-binding EF-hand family protein |
| AT2G44940 | 7.88 | 6.32 | 20.17 | 28.83 | Integrase-type DNA-binding | |