Table 1. Candidate genes for host-specific differential gene expression in of R. solanacearum strains UW163 (Moko) and IBSBF1503 (NPB).
Log2FC values are indicated for each plant vs. plant comparison (condition 1 vs. condition 2). Bold-faced numbers indicate values within our −2 > log2FC > 2 threshold for differentially expressed genes. Genes with negative and positive Log2FC are up-regulated in conditions 1 and conditions 2, respectively. M-Tom or N-Tom: Moko or NPB strain extracted from tomato; M-Ban: Moko strain extracted from banana; N-Mel: NPB strain extracted from melon.
| Gene | Product | M-Tom. vs. M-Ban. (log2 FC) | N-Tom. vs. N-Mel. (log2 FC) | M-Tom. vs. N-Tom. (log2 FC) | M-Ban. vs. N-Mel. (log2 FC) | |
|---|---|---|---|---|---|---|
| exuT2 | Putative hexuronate transporter | 0.45 | −2.38 | −3.72 | −6.57 | |
| katB | Catalase | −0.97 | 0.46 | 4.63 | 6.05 | |
| Iron acquisition | fur | Ferric uptake regulator | 2.75 | 0.00 | 0.00 | −2.07 |
| fyuA | TonB-dependent siderophore receptor | 3.80 | 0.00 | 0.00 | −3.83 | |
| irp | Siderophore biosynthesis (NRPS domains) | 4.20 | 0.00 | −0.51 | −4.14 | |
| pchG | Siderophore biosynthesis (thiazolinyl imide reductase) | 4.67 | 0.00 | 0.00 | −4.39 | |
| angT | Putative anguibactin biosynthesis (thioesterase) | 4.42 | 0.00 | 0.00 | −4.18 | |
| Microaeroby metabolism | ccoN | Cytochrome C oxidase cbb3-type | −3.70 | 0.55 | −1.04 | 3.21 |
| ccoO | Cytochrome C oxidase cbb3-type | −6.06 | 0.72 | −1.61 | 5.16 | |
| ccoQ | Cytochrome C oxidase cbb3-type | −5.67 | 0.87 | −2.01 | 4.51 | |
| ccoP | Cytochrome C oxidase cbb3-type | −5.14 | 0.57 | −1.26 | 4.45 | |
| Type III effectors | ripO1 | Type III effector, HopG1 family | −2.44 | 0.00 | 1.26 | 3.89 |
| ripP1 | Type III effector PopP1 | −0.65 | 0.00 | 1.56 | 2.25 | |
| ripP2 | Type III effector PopP2 | −1.04 | −0.43 | 2.45 | 3.05 | |
| ripC2 | Type III effector | −0.70 | 0.00 | 3.73 | 4.27 | |
| ripY | Type III effector (ankyrin repeats) | −1.00 | 0.00 | 0.80 | 2.21 | |
| ripS4 | Type III effector SKWP4 | −3.00 | 0.00 | 0.00 | 2.89 | |
| ripE2 | Type III effector (Xcc1246-like) | −1.55 | 0.00 | 1.63 | 2.96 | |
| ripD | Type III effector (AvrPphD family) | −0.78 | 0.00 | 1.29 | 2.32 | |
| ripX | Type III effector (harpin) | −1.86 | 0.00 | 0.93 | 2.88 | |
| ripAB | Type III effector | −2.21 | 0.00 | 1.22 | 3.31 | |
| ripAC | Type III effector (LRR domain) | −1.10 | 0.00 | 1.20 | 2.14 | |
| Nitrate assimilation | nirB | Assimilatory nitrite reductase | 0.00 | 0.00 | −1.67 | −2.37 |
| nirD | Assimilatory nitrite reductase | 0.00 | 0.00 | −2.35 | −2.08 | |
| narK3 | ATP-independent high-affinity nitrate transporter | 0.00 | −1.02 | −1.10 | −2.59 | |
| Denitrification | narK1 | NO3- ABC transporter protein | −6.88 | 0.84 | −1.27 | 6.44 |
| narK2 | NO3- ABC transporter protein | −6.43 | 0.98 | −1.37 | 6.05 | |
| narG | NO3- reductase | −5.75 | 0.00 | −1.07 | 5.24 | |
| narH | NO3- reductase | −5.05 | 0.00 | −1.04 | 4.47 | |
| narI | NO3- reductase | −4.85 | 0.00 | −1.06 | 4.30 | |
| narJ | NO3- reductase | −5.16 | 0.00 | −1.22 | 4.48 | |
| narX | NO3- sensor kinase | −4.21 | 0.00 | −0.96 | 3.34 | |
| narL | NO3- response regulator | −3.62 | 0.45 | −0.97 | 3.09 | |
| hmp | Flavohemoprotein, NO dioxygenase | −4.87 | 0.72 | −0.58 | 4.99 | |
| aniA | NO2- reductase | −7.37 | 0.00 | −1.55 | 6.29 | |
| norB | NO reductase | −5.47 | 0.87 | −0.93 | 5.41 |