| Summary: | The Ascomycete <i>Ophiostoma novo-ulmi</i> threatens elm populations worldwide. The molecular mechanisms underlying its pathogenicity and virulence are still largely uncharacterized. As part of a collaborative study of the <i>O. novo-ulmi</i>-elm interactome, we analyzed the <i>O. novo-ulmi</i> ssp. <i>americana</i> transcriptomes obtained by deep sequencing of messenger RNAs recovered from <i>Ulmus americana</i> saplings from one resistant (Valley Forge, VF) and one susceptible (S) elm genotypes at 0 and 96 h post-inoculation (hpi). Transcripts were identified for 6424 of the 8640 protein-coding genes annotated in the <i>O. novo-ulmi</i> nuclear genome. A total of 1439 genes expressed in planta had orthologs in the PHI-base curated database of genes involved in host-pathogen interactions, whereas 472 genes were considered differentially expressed (DEG) in S elms (370 genes) and VF elms (102 genes) at 96 hpi. Gene ontology (GO) terms for processes and activities associated with transport and transmembrane transport accounted for half (27/55) of GO terms that were significantly enriched in fungal genes upregulated in S elms, whereas the 22 GO terms enriched in genes overexpressed in VF elms included nine GO terms associated with metabolism, catabolism and transport of carbohydrates. Weighted gene co-expression network analysis identified three modules that were significantly associated with higher gene expression in S elms. The three modules accounted for 727 genes expressed in planta and included 103 DEGs upregulated in S elms. Knockdown- and knockout mutants were obtained for eight <i>O. novo-ulmi</i> genes. Although mutants remained virulent towards <i>U. americana</i> saplings, we identified a large repertoire of additional candidate <i>O. novo-ulmi</i> pathogenicity genes for functional validation by loss-of-function approaches.
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