Table 4.
Genes with isolate‐specific expression profiles during wheat infection
| Genes differentially expressed between isolatesa | 2,377 genes in total | ||
| 22.8% of all 10,426 core genes | |||
| Comparison (all four stages) | DE genes b | Regulation | |
| Zt05‐Zt09 | 1,311 | ↑Zt05: 917 ↑Zt09: 436 | |
| Zt05‐Zt10 | 1,482 | ↑Zt05: 1086 ↑Zt10: 412 | |
| Zt09‐Zt10 | 1,514 | ↑Zt09: 1062 ↑Zt10: 541 | |
| GO groups enrichedc | GO term | DE genes in GO group | GO ID |
| Transmembrane transport | 159 (of 491) | GO:0055085 | |
| Carbohydrate metabolic process | 82 (of 242) | GO:0005975 | |
| Proteolysis | 64 (of 237) | GO:0006508 | |
| Amino acid transmembrane transport | 17 (of 36) | GO:0003333 | |
| Oxidation–reduction process | 159 (of 627) | GO:0055114 | |
| Lipid catabolic process | 6 (of 15) | GO:0016042 | |
| Candidate secreted effector genes | 245 of 370 effector candidate genes | ||
| Comparison (all four stages) | DE effector genes d | Regulation | |
| Zt05‐Zt09 | 161 | ↑Zt05: 120 ↑Zt09: 50 | |
| Zt05‐Zt10 | 167 | ↑Zt05: 141 ↑Zt10: 31 | |
| Zt09‐Zt10 | 193 | ↑Zt09: 167 ↑Zt10: 60 | |
DE: differentially expressed. ↑: significantly up‐regulated in the isolate.
Summary of genes that are differentially expressed between the three Z. tritici isolates Zt05, Zt09, and Zt10 during the four infection stages.
a
Differentially expressed genes identified by DESeq2, p adj ≤0.01, |log2 fold change| ≥2.
b
774 genes are differentially expressed in at least two isolate comparisons.
c
Gene Ontology (GO) group enrichment analyses by topGO for ontology “Biological Process,” p ≤ 0.01.
d
198 effector candidate genes are differentially expressed in at least two isolate comparisons.