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

Date

2022

Authors

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.

Journal Title

Journal ISSN

Volume Title

Publisher

Journal of Fungi

Abstract

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.

Description

Keywords

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

Citation

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. https://doi.org/10.3390/jof8060637