Comparative analysis of transcriptomes of Ophiostoma novo-ulmi ssp. americana colonizing resistant or sensitive genotypes of American elm




Nigg, Martha
de Oliveira, Thais C.
Sarmiento-Villamil, Jorge L.
de la Bastide, Paul Y.
Hintz, William E.
Sherif, Sherif M.
Shukla, Mukund
Bernier, Louis
Saxena, Praveen K.

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Journal of Fungi


The Ascomycete Ophiostoma novo-ulmi threatens elm populations worldwide. The molecular mechanisms underlying its pathogenicity and virulence are still largely uncharacterized. As part of a collaborative study of the O. novo-ulmi-elm interactome, we analyzed the O. novo-ulmi ssp. americana transcriptomes obtained by deep sequencing of messenger RNAs recovered from Ulmus americana 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 O. novo-ulmi 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 O. novo-ulmi genes. Although mutants remained virulent towards U. americana saplings, we identified a large repertoire of additional candidate O. novo-ulmi pathogenicity genes for functional validation by loss-of-function approaches.



Dutch elm disease, Ophiostoma novo-ulmi, RNA-Seq, pathogenicity, virulence, mutants


Nigg, M., de Oliveira, T., Sarmiento-Villamil, J., de la Bastide, P., Hintz, W., . . . Saxena, P. (2022). “Comparative analysis of transcriptomes of Ophiostoma novoulmi ssp. americana colonizing resistant or sensitive genotypes of American elm.” Journal of Fungi, 8(6), 637.