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, Centre for Forest Biology
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