Table I.
Number of genes categorized according to known or suspected involvement in feeding site and gall formation
All Array Genes and All Significant Genes are all genes used on tomato root gene array and all genes statistically determined to be regulated (at q ≤ 0.05) in tissue comparisons, respectively. Statistical comparisons of Mixed-Stage Infection, Onset of RKN Reproduction, and Resistant Infected are made to uninfected tissue. Mixed-stage roots are nonsynchronous infected roots (grown in a greenhouse). Categories are based as follows: 1, all genes on the array; 2, hormones (Hutangura et al., 1999; Bird and Koltai, 2000); 3, pathogenesis-related genes (Bowles, 1990); 4, transport (Hammes et al., 2005); 5, nucleic acid binding; 6, (I) shikimate (Doyle and Lambert, 2002); 7, (Y) cell cycle (Niebel et al., 1996; de Almeida Engler et al., 1999); 8, aquaporin, water channel-related genes (Opperman et al., 1994); 9, (X) peroxidase; 10, cell wall (Bird,1974); 11, GC genes (Wilson et al., 1994); 12, (S) ribosome-related genes; and 13, genes with unknown function. Annotations were searched with keywords (Supplemental Table S2) to identify genes to categorize.
| Array Probes | All1 | H2 | P3 | T4 | B5 | I6 | Y7 | A8 | X9 | W10 | GC11 | S12 | U13 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All Array Genes | 1,547 | 20 | 13 | 33 | 22 | 4 | 9 | 8 | 8 | 14 | 181 | 75 | 318 |
| All Significant Genes | 753 | 8 | 7 | 19 | 8 | 4 | 5 | 7 | 6 | 4 | 96 | 59 | 146 |
| Mixed-Stage Infection | 258 | 5 | 2 | 7 | 2 | 3 | 4 | 2 | 3 | 2 | 25 | 7 | 50 |
| Onset of RKN Reproduction | 264 | 4 | 4 | 9 | 3 | 1 | 1 | 5 | 5 | 1 | 34 | 15 | 41 |
| All Infected (between 12 and 36 hpi) | 354 | 3 | 4 | 8 | 3 | 1 | 2 | 2 | 1 | 2 | 53 | 51 | 64 |
| Susceptible Infected (between 12 and 36 hpi) | 217 | 3 | 2 | 6 | 1 | 0 | 1 | 2 | 1 | 1 | 31 | 43 | 38 |
| Resistant Infected | 58 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 1 | 0 | 6 | 4 | 12 |