Table 3.
Phenotypes of knockdown- and knockout mutants of Ophiostoma novo-ulmi in vitro and in planta.
| Strain | Gene | Annotation | PHI: Base | Method 1 | %RGE 2 | Nb Transcripts 3 | DEG 4 | Module 5 | Mycelial Gowth 6 | Virulence 7 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 96_S | 96_VF | MEA | NaCl | Lim | Apple | Elm | ||||||||
| Cyp570-A4D | 7411 | Pisatin demethylase | − | RNAi | 25.3 | 5.0 | 0.0 | Up96_S | Gre | 131.3 8 | n.t. 9 | 81.0 * | 97.0 | 96.3 |
| Cyp52P6-AD | 7466 | Putative α-Pinene to Verbenol enzyme | − | RNAi | 3.4 | 17.3 | 1.0 | Up96_S | Pur | 117.8 | n.t. | 69.0 * | 105.0 | 87.5 |
| Hex1-D | 6790.1 | Hex1 Woronin body formation | 1591 | RNAi | 6.5 | 389.7 | 97.0 | No | Gre | 78.0 * | 45.2 * | 53.7 * | 55.0 * | 100.6 |
| Mad1-J | 3773 | Mad1 Adhesin | − | RNAi | 2.8 | 10.3 | 4.3 | No | Mag | 128.5 * | 145.2 * | 108.9 | 84.0 | 101.0 |
| AmtA-B | 282 | Ammonium transporter | 2710 | RNAi | 1.6 | 13.3 | 0.0 | Up96_S | Pur | 109.2 | n.t. | n.t. | 109.0 | 101.0 |
| ΔAox1 5-1 | 5955 | Aox1 Alcohol oxidase | 199 | OSCAR | n.t. | 567.3 | 808.0 | Up96_VF | GrY | 84.9 * | n.t. | n.t. | 62.2 * | 74.2 |
| ΔOpf2 1-29 | 1642 | Opf2 Transcription Factor | 1931 | OSCAR | n.t. | 33.0 | 16.0 | No | GrY | 100.7 | n.t. | n.t. | 69.4 * | 100.1 |
| ΔBct2 3-12 | 2340 | Bct2 Transcription Factor | 1933 | OSCAR | n.t. | 20.3 | 4.0 | No | Ora | 81.6 * | n.t. | n.t. | 96.9 | 100.2 |
1 Knockdown (RNAi) mutants were derived from O. novo-ulmi ssp. novo-ulmi H327, whereas knockout (OSCAR) mutants were obtained from strain O. novo-ulmi ssp. novo-ulmi Δmus52-1O. Both strains were highly virulent on Golden Delicious (GD) apples and Ulmus americana saplings. 2 % Residual gene expression measured in knockdown mutants compared to H327 progenitor. 3 Ophiostoma novo-ulmi ssp. americana MH74-4O transcripts detected in susceptible (96_S) or resistant (96_VF) saplings of Ulmus americana at 96 h post-inoculation. 4 Differentially expressed genes (DEGs) were significantly more expressed either in susceptible elms (Up96_S elm) or in VF elms (Up96_VF elm). 5 Modules determined by Weighted Gene Co-expression Newtork Analysis (WGCNA): Gre: Green; Pur: Purple; Mag: Magenta; GrY: Green Yellow; Ora: Orange. 6 MEA: Malt extract agar; NaCl: MEA supplemented with 0.2 M NaCl; Lim: MEA supplemented with 1:1000 limonene. 7 Virulence on GD apples was assessed by measuring the diameter of necrosis after 4 weeks. Virulence on elms was assessed by mesuring the % defoliation of American elm saplings after 3 weeks. 8 Data for mycelial growth, and virulence on GD apples and U. americana saplings are presented as % of values recorded for progenitor strains H327 (for RNAi mutants) or Δmus52-1O (for OSCAR mutants). 9 n.t.: not tested. * indicates significant difference (p < 0.05) between mutant and progenitor strain.