Comparative Analysis of Transcriptomes of Ophiostoma novo-ulmi ssp. americana Colonizing Resistant or Sensitive Genotypes of American Elm

• Published in: Journal of fungi (Basel) Vol. 8; no. 6; p. 637
• Main Authors: Nigg, Martha, de Oliveira, Thais C, Sarmiento-Villamil, Jorge L, de la Bastide, Paul Y, Hintz, Will E, Sherif, Sherif M, Shukla, Mukund, Bernier, Louis, Saxena, Praveen K
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.06.2022; MDPI
• Subjects: Carbohydrates; Comparative analysis; CRISPR; Dutch elm disease; Fungi; Gene expression; Genes; Genomes; Genotypes; Host-pathogen interactions; Inoculation; Molecular modelling; Mutants; Ophiostoma novo-ulmi; Pandemics; Pathogenicity; Pathogens; RNA-Seq; Transcriptomes; Ulmaceae; Virulence; Canada; Quebec Canada; pathogenicity; Dutch elm disease; Ophiostoma novo-ulmi; virulence; RNA-Seq; mutants
• ISSN: 2309-608X; 2309-608X
• DOI: 10.3390/jof8060637

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