Table 1.
Orthologous gene comparisons between 5-week-old lumichrome-treated lotus (L. japonicus) and tomato (S. lycopersicum) roots.
|
L. japonicus |
S. lycopersicum |
AGI code | A. thaliana functional annotation | ||||
|---|---|---|---|---|---|---|---|
| Array ID | logFC | Adj. P-value | Array ID | logFC | Adj. P-value | ||
| PHYTOHORMONE METABOLISM | |||||||
| chr5.CM0052.19_at | −1.89 | 0.031 | 4.1.18.1 | −2.64 | 0.011 | At5g64750 | ABA repressor 1 |
| chr6.CM0114.20_at | −3.44 | 0.016 | At1g28360 | Ethylene response factor12 (ERF12) | |||
| chr5.CM0909.73_at | −6.22 | 0.007 | At5g61590 | Ethylene-responsive element binding factor-like | |||
| chr4.CM0288.8_at | −2.38 | 0.064 | 6.1.16.2 | −3.72 | 0.02 | At1g05010 | 1-Aminocyclopropane-1-carboxylate oxidase |
| chr3.TM1367.15_at | 2.64 | 0.019 | 5.1.3.12 | 1.92 | 0.04 | At2g41310 | Putative two-component response regulator 3 protein |
| chr5.CM0335.12_at | −4.31 | 0.017 | 8.4.19.1 | −3.11 | 0.04 | At1g20510 | 4-Coumarate:CoA ligase (OPCL1) |
| TRANSCRIPTION FACTOR (-LIKE) | |||||||
| chr2.CM0132.7_at | 4.85 | 0.021 | 2.3.10.17 | 5.81 | 0.007 | At4g37730 | bZip transcription factor 7(AtbZip7) |
| chr4.CM0227.6_at | −9.95 | 0.028 | 2.1.19.2 | −3.11 | 0.03 | At4g34410 | AP2 domain-containing transcription factor |
| chr5.CM0311.11_at | 2.26 | 0.013 | 4.4.14.11 | 4.55 | 0.04 | At1g31050 | AtbHLH111 |
| Ljwgs_064987.2_at | −6.02 | 0.001 | 7.3.19.10 | −2.41 | 0.04 | At4g27280 | Ca2 + binding EF hand family protein |
| chr3.TM1463.16_at | 1.77 | 0.018 | 5.4.2.3 | 1.87 | 0.03 | At5g54630 | Zinc finger related protein |
| Ljwgs_020980.2_at | −8.48 | 0.03 | 8.4.20.16 | −8.97 | 0.04 | At2g37430 | Putative C2H2-type zinc finger protein |
| CARBOHYDRATE METABOLISM | |||||||
| chr1.CM0222.6_at | 3.83 | 0.008 | 8.4.10.12 | 4.56 | 0.04 | At1g12900 | Glyceraldehyde 3-phosphate dehydrogenase A (GAPA-2) |
| chr1.CM0113.81_at | 3.26 | 0.011 | At1g42970 | Glyceraldehyde 3-phosphate dehydrogenase (GAPB) | |||
| Ljwgs_054325.1_at | −3.77 | 0.0004 | 8.2.19.12 | −1.7 | 0.05 | At3g15350 | Glycosyltransferase family 14 |
| chr2.CM0102.62_at | −5.62 | 0.007 | 5.4.19.4 | −2.7 | 0.02 | At3g22250 | UDP-glucoronosyl/-glucosyl transferase |
| Ljwgs_031056.1_at | 1.96 | 0.021 | 2.2.7.6 | 4.94 | 0.009 | At5g38430 | RuBisCO small subunit 1b |
| chr2.TM1655.9_at | 4.98 | 0.001 | 8.3.12.20 | 2.17 | 0.04 | At1g67090 | RuBisCO like protein, small subunit |
| Ljwgs_031056.1_at | 1.96 | 0.021 | At5g38430 | RuBisCO small chain 1b precursor | |||
| chr5.TM1574.11_at | 3.51 | 0.002 | 8.1.9.9 | 9.65 | 0.02 | At2g30570 | Photosystem II reaction center 6.1KD protein |
| chr2.TM1655.9_at | 4.98 | 0.001 | 5.4.7.9 | 7.08 | 0.05 | At1g67090 | RuBisCO like protein, small subunit |
| Ljwgs_057808.1_at | 1.71 | 0.012 | 4.2.10.10 | 7.18 | 0.04 | At5g54190 | NADPH:protochlorophyllide oxidoreductase A (PORA) |
| FATTY ACID METABOLISM | |||||||
| chr3.CM0135.11_at | 1.81 | 0.029 | 2.4.15.7 | 2.76 | 0.01 | At2g05990 | Enoyl-ACP reductase (ENR1) |
| MISCELLANEOUS | |||||||
| TM0802.5_at | 3.84 | 0.015 | 6.2.1.16 | 3.98 | 0.008 | At5g65360 | Histone H3 |
| chr5.TM0431.19_at | −2.13 | 0.014 | 8.2.17.12 | −2.56 | 0.05 | At1g10390 | Nucleoporin family |
| chr5.TM0431.19_at | −2.13 | 0.014 | 7.1.19.6 | −3.27 | 0.02 | At1g10390 | Nucleoporin family |
| Ljwgs_042055.1_at | −11.2 | 0.027 | 8.4.17.18 | −2.87 | 0.04 | At1g43710 | Histidine decarboxylase, embryo defective 1075 |
| chr1.TM0811.11_at | −3.71 | 0.056 | 6.1.19.5 | −5.64 | 0.02 | At4g02380 | Senescence associated gene 12 (SAG12) |
| chr1.CM0104.34_at | −5.99 | 0.007 | 8.1.16.1 | −4.43 | 0.03 | At5g18270 | NAM (no apical meristem)-like protein |
| chr1.CM0349.17_at | −11.4 | 0.023 | 5.1.13.1 | −4.01 | 0.01 | At1g14560 | Mitochondrial carrier like protein |
| Ljwgs_018600.1_at | −2.09 | 0.049 | At1g20860 | Putative inorganic phosphate transporter protein | |||
| Ljwgs_020324.1_at | −3.21 | 0.03 | 7.2.19.14 | −2.81 | 0.03 | At5g53130 | Cyclic nucleotide-regulated ion channel |
| chr1.TM1573.13.1_at | −2.98 | 0.021 | 8.3.19.13 | −4.03 | 0.02 | At3g24550 | ATP binding protein kinase, AtPERK1 |
| UNKNOWN | |||||||
| chr3.CM0142.58_at | −3.49 | 0.049 | 8.1.20.1 | −6.95 | 0.003 | At3g15810 | Unknown protein |
| chr3.CM0142.58_at | −3.49 | 0.049 | 8.2.17.16 | −3.55 | 0.004 | At3g15810 | Unknown protein |
| chr1.CM0181.3_s_at | 1.85 | 0.005 | 5.1.4.16 | 4.97 | 0.02 | At1g21680 | Unknown protein |
| chr2.CM0608.80_at | −2.6 | 0.038 | 1.2.17.11 | −5.29 | 0.03 | At1g27100 | Unknown protein |
| Ljwgs_054723.1_at | −2.44 | 0.032 | 7.1.19.9 | −2.05 | 0.04 | At3g26580 | Unknown protein |
Values are represented as log2 fold changes (logFC) of gene expressions normalized to control roots of three independent hybridizations and the P value adjusted (adj. P value) to correct for the probability of false positives using the FDR correction (Benjamini and Hochberg, 1995; P value <0.05 was deemed significant). Gene annotations was based on probe oligosequence similarity to the Arabidopsis genome, and represented by the Arabidopsis genome initiative (AGI) code.