Table 4.
P. graminis f. sp. tritici genes that are predicted to undergo site-specific diversifying selection with significant in planta up-regulation (wheat infection to germinated urediniospores, p < 0.05, fold change > 2) and a fold change > 2 when comparing isolated haustoria to germinated urediniospores.
| Pathogen-associated cluster | Protein | Secretion signal | aas | Cys | Rust orthologs | PFAM domain | Wheat/Spores (FC) | Haustoria/Spores (FC) |
|---|---|---|---|---|---|---|---|---|
| C11 | PGTG_08638 | Yes | 292 | 1 | Stripe, leaf | – | 187.1 | 1085.9 |
| Fungal | PGTG_16225 | Yes | 310 | 7 | Stripe, leaf | – | 43.8 | 239 |
| C11 | PGTG_04972 | – | 340 | – | Stripe, leaf | – | 21.8 | 147.7 |
| No gene family | PGTG_14091 | Yes | 502 | 1 | Stripe, leaf | – | 25.8 | 145.5 |
| C12 | PGTG_09276 | – | 134 | – | Stripe | – | 4.7 | 142.4 |
| C6 | PGTG_05592 | Yes | 257 | 10 | Stripe | – | 48.2 | 118.7 |
| C1 | PGTG_05174 | – | 239 | 1 | Stripe, leaf, flax | – | 32.6 | 81.2 |
| C6 | PGTG_11727 | Yes | 336 | 11 | Stripe | – | 9 | 56 |
| C2 | PGTG_06244 | Yes | 277 | 1 | Leaf | – | 4.2 | 53.7 |
| Fungal | PGTG_17076 | – | 67 | – | Stripe, leaf | Seed maturation protein (PF04927, 2.9e-07) | 118.8 | 50.8 |
| C6 | PGTG_03859 | Yes | 165 | 11 | Stripe, leaf | – | 19.8 | 44.8 |
| C11 | PGTG_16303 | Yes | 441 | 4 | Stripe | – | 3.1 | 31.6 |
| C8 | PGTG_10538 | Yes | 411 | – | Stripe, leaf | – | 31.9 | 31.6 |
| C8 | PGTG_10539 | Yes | 392 | 2 | Leaf | – | 13.9 | 30.1 |
| C10 | PGTG_09318 | Yes | 87 | 8 | Stripe, leaf | – | 77 | 19.2 |
| C11 | PGTG_00341 | – | 361 | 2 | Stripe, leaf | – | 4.9 | 16.6 |
| C2 | PGTG_10398 | – | 1011 | 3 | Stripe, leaf | – | 22.8 | 13.5 |
| C11 | PGTG_14389 | – | 298 | 1 | Stripe | – | 3.9 | 11.4 |
| C6 | PGTG_17308 | Yes | 125 | 7 | Stripe | – | 5.9 | 8.3 |
| C4 | PGTG_01642 | – | 1329 | 2 | Stripe, leaf | – | 2.7 | 7.3 |
| C11 | PGTG_10056 | Yes | 766 | 12 | Stripe, leaf | – | 37.1 | 7.3 |
| C7 | PGTG_03213 | – | 565 | – | Stripe, leaf | – | 25.6 | 7.2 |
| C11 | PGTG_15791 | – | 376 | 4 | Stripe | – | 2.7 | 7.2 |
| C8 | PGTG_13414 | Yes | 197 | 2 | Stripe, leaf | – | 45.8 | 6.6 |
| C4 | PGTG_01631 | Yes | 807 | 5 | Stripe, leaf | – | 7.5 | 5.6 |
| C11 | PGTG_15481 | Yes | 502 | 3 | Stripe, leaf | – | 2.3 | 5.6 |
| C11 | PGTG_17733 | Yes | 482 | – | Leaf | – | 9.5 | 5.3 |
| C8 | PGTG_10625 | Yes | 474 | 3 | Stripe | – | 5 | 5.3 |
| C11 | PGTG_18622 | – | 300 | 2 | Stripe, leaf | – | 2.5 | 4.9 |
| C2 | PGTG_07786 | – | 854 | 3 | Stripe, leaf | – | 2.6 | 4.4 |
| C11 | PGTG_12173 | – | 629 | 4 | Stripe, leaf | – | 6.1 | 3.9 |
| C2 | PGTG_07911 | Yes | 324 | 4 | Stripe, leaf | – | 7 | 3.9 |
| C6 | PGTG_16750 | Yes | 124 | 8 | Leaf | – | 4.1 | 3.8 |
| C6 | PGTG_04109 | Yes | 100 | 9 | Leaf | – | 5.1 | 3.8 |
| C6 | PGTG_05119 | Yes | 141 | 6 | Stripe, leaf | – | 61.3 | 3.7 |
| Fungal | PGTG_05197 | – | 537 | 9 | Leaf | Sugar (and other) transporter (PF00083, 3e-76) | 5.7 | 3.7 |
| C7 | PGTG_07078 | – | 324 | – | Stripe, leaf, flax | Ribosomal protein S10p/S20e (PF00338, 1.2e-16) | 2.6 | 3.2 |
| C12 | PGTG_17001 | – | 878 | 13 | Stripe, leaf | – | 2.6 | 3 |
| C11 | PGTG_15702 | – | 334 | 15 | Stripe, leaf, flax, poplar | – | 2.3 | 2.8 |
| C3 | PGTG_06359 | – | 734 | 13 | Stripe, leaf | – | 6.2 | 2.7 |
| C6 | PGTG_17534 | Yes | 114 | 4 | Stripe | – | 18.1 | 2.4 |
| C11 | PGTG_14388 | Yes | 353 | 1 | Leaf | – | 2.5 | 2.2 |
| C9 | PGTG_19205 | – | 299 | 5 | Leaf | – | 9.7 | 2.1 |
| C9 | PGTG_14673 | Yes | 189 | 10 | Stripe | – | 6.4 | 2.1 |
| C11 | PGTG_15389 | – | 667 | 2 | Leaf | – | 2.2 | 2.1 |
| C8 | PGTG_10832 | – | 149 | 3 | Leaf | – | 2 | 2 |
| C12 | PGTG_17927 | – | 711 | 9 | Stripe | Alpha-kinase family (PF02816,1.4e-32) | 5.5 | 2 |
For each protein, its signal peptide prediction by Signal P 4.1, protein sequence length (aas), number of cysteines (Cys) and distribution of wheat stem rust orthologs across the Pucciniomycotina genomes are given. Stripe stands for P. striiformis PST-78, leaf for P. triticina 1-1 BBBD Race 1, flax for M. lini and poplar for M. laricis-populina. Note that no proteins undergoing diversifying selection were found in pathogen-associated cluster C5. Protein expression levels are given for the two experiments (FC: fold change). The genes are ordered by decreasing haustorial differential expression fold change.