Table 2.
Fold changes (nodule over root) and adjusted p-values of symbiotic pathway genes.
| Gene Name | MergedOrtho Group |
C. thyrsiflorus ortholog |
D. glomerata ortholog |
M.
truncatula/L.
japonicus ortholog |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene ID | Log2FC | P-value | Gene ID | Log2FC | P-value | Gene ID | Log2FC | P-value | GenBank ID | ||
| NFR1 | – | Ct_CtTrNR03429 | -0.37 | 0.151 | Dg_DgTrNR03578 | 2.75 | 0.000 | Mt_Medtr5g 086130 | -2.10 | 0.000 | AY372406.1 |
| Dg_DgTrNR03579 | -1.39 | 0.000 | |||||||||
| Dg_DgTrNR03580 | 2.54 | 0.000 | |||||||||
| NFR5 | – | Ct_CtTrNR01660, Ct_CtTrNR02016, Ct_CtTrNR02556, Ct_CtTrNR03429, Ct_CtTrNR03658, Ct_CtTrNR10088, Ct_CtTrNR13226, Ct_CtTrNR13284, Ct_CtTrNR14238, Ct_CtTrNR14293 |
Dg_DgTrNR09631 | -1.52 | 0.000 | Mt_Medtr5g019040 | -2.43 | 0.000 | DQ496250.1 | ||
| SYMRK | MergedOrthoGroup005636 | Ct_CtTrNR07134 | -0.19 | 0.413 | Dg_DgTrNR12393 | 0.46 | 0.000 | Mt_Medtr5g030920 | 0.60 | 0.002 | AF491998.1 |
| SYMREM | MergedOrthoGroup006520 | Ct_CtTrNR08408 | 2.10 | 0.003 | Dg_DgTrNR05672 | 5.65 | 0.000 | Mt_Medtr5g010590 | -0.22 | 0.775 | – |
| Mt_Medtr8g097320 | 9.88 | 0.000 | JQ061257.1 | ||||||||
| HMGR | – | Ct_CtTrNR06569, Ct_CtTrNR06801, Ct_CtTrNR08716, Ct_CtTrNR12229 |
Dg_DgTrNR07804, Dg_DgTrNR14611, Dg_DgTrNR14612 |
Mt_Medtr5g087550 | -1.35 | 0.000 | XM_003617018.2 | ||||
| NUP85 | MergedOrthoGroup003212 | Ct_CtTrNR03893 | -0.87 | 0.020 | Dg_DgTrNR02299 | 0.12 | 0.132 | Mt_Medtr1g006690 | -0.19 | 0.665 | XM_003588338.2 |
| NUP133 | MergedOrthoGroup009404 | Ct_CtTrNR12969 | -0.20 | 0.263 | Dg_DgTrNR15290 | 0.58 | 0.000 | Lj_Lj2g3v3337540 | – | – | AJ890251.1 |
| Lj_Lj0g3v0050449 | – | – | |||||||||
| Mt_Medtr5g097260 | -0.48 | 0.064 | – | ||||||||
| CASTOR | MergedOrthoGroup008762 | Ct_CtTrNR11902 | -0.39 | 0.071 | Dg_DgTrNR14656 | 0.37 | 0.001 | Mt_Medtr7g117580 | -0.23 | 0.431 | FJ974130.1 |
| POLLUX | MergedOrthoGroup009011 | Ct_CtTrNR12292 | -0.43 | 0.090 | Dg_DgTrNR14917 | -0.83 | 0.000 | Mt_Medtr2g005870 | 1.61 | 0.000 | AY497771.1 |
| CCAMK | MergedOrthoGroup006145Sub001 | Ct_CtTrNR07875 | -0.49 | 0.064 | Dg_DgTrNR14486 | 0.02 | 0.857 | Mt_Medtr8g043970 | 0.59 | 0.004 | AY496049.1 |
| CYCLOPS | MergedOrthoGroup005459Sub002 | Ct_CtTrNR09813 | 0.25 | 0.294 | Dg_DgTrNR00459 | 1.60 | 0.000 | Mt_Medtr5g026850 | 3.18 | 0.000 | EF117279.1 |
| NSP1 | MergedOrthoGroup009317 | Ct_CtTrNR12805 | -0.10 | 0.595 | Dg_DgTrNR11911 | 0.96 | 0.000 | Mt_Medtr3g085310 | 0.00 | 1.000 | – |
| Mt_Medtr8g020840 | 1.62 | 0.000 | AJ972478.1 | ||||||||
| NSP2 | MergedOrthoGroup000090 | Ct_CtTrNR00101 | 0.50 | 0.232 | Dg_DgTrNR00363 | -1.38 | 0.000 | Mt_Medtr3g072710 | -1.34 | 0.000 | AJ832138.1 |
| Dg_DgTrNR01580 | 0.99 | 0.001 | Mt_Medtr5g058860 | -2.59 | 0.000 | – | |||||
| ERN1 | MergedOrthoGroup010414 | Ct_CtTrNR15219 | -2.56 | 0.003 | Dg_DgTrNR02845 | -0.66 | 0.006 | Mt_Medtr6g029180 | -2.53 | 0.000 | – |
| Dg_DgTrNR10008 | 4.95 | 0.000 | Mt_Medtr7g085810 | -0.39 | 0.373 | EU038802.2 | |||||
| NIN | MergedOrthoGroup008966 | Ct_CtTrNR12221 | 5.48 | 0.003 | Dg_DgTrNR00885 | 8.30 | 0.000 | Mt_Medtr5g099060 | 7.42 | 0.000 | FJ719774.1 |
| Ct_CtTrNR12222 | 6.47 | 0.004 | Dg_DgTrNR00886 | 7.56 | 0.000 | ||||||
| LHK1 | MergedOrthoGroup007561 | Ct_CtTrNR09972 | 1.16 | 0.156 | Dg_DgTrNR03717 | -0.92 | 0.000 | Lj_Lj0g3v0108729 | – | – | DQ848999.1 |
| Mt_Medtr2g067240 | 0.00 | 1.000 | – | ||||||||
| Mt_Medtr5g044100 | 0.00 | 1.000 | – | ||||||||
| Mt_Medtr8g106150 | -0.22 | 0.524 | – | ||||||||
| PIR | – | Ct_CtTrNR13403 | 0.13 | 0.688 | Dg_DgTrNR01709 | 0.17 | 0.048 | Lj_Lj1g3v5020900 | – | – | AM946364.1 |
| Dg_DgTrNR07598 | -0.51 | 0.000 | |||||||||
| RPG | MergedOrthoGroup006667Sub001 | Ct_CtTrNR08628 | -0.78 | 0.022 | Dg_DgTrNR05600 | 8.90 | 0.000 | Mt_Medtr1g090807 | 6.45 | 0.000 | DQ854741.1 |
| Ct_CtTrNR14741 | 5.14 | 0.003 | Dg_DgTrNR07056 | -0.25 | 0.102 | ||||||
| CERBERUS | MergedOrthoGroup002490Sub002 | Ct_CtTrNR11435 | 0.24 | 0.265 | Dg_DgTrNR05473 | 0.87 | 0.000 | Mt_Medtr1g090320 | 1.25 | 0.000 | EU926661.1 |
For each symbiotic pathway gene, the corresponding MergedOrthoGroup and the ortholog(s) are shown. Each ortholog also has its log2-fold change and adjusted p-values are indicated. The yellow cells are not orthologs, but are putative homologs found by OrthoReD. All genes included in this table were selected from Kouchi et al. (2010) and/or Oldroyd (2013).