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

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.

SUBMITTER: Nigg M

PROVIDER: S-EPMC9224576 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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

Nigg Martha M de Oliveira Thais C TC Sarmiento-Villamil Jorge L JL de la Bastide Paul Y PY Hintz Will E WE Sherif Sherif M SM Shukla Mukund M Bernier Louis L Saxena Praveen K PK

Journal of fungi (Basel, Switzerland) 20220616 6

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 genotype ...[more]

PMID: 35736120

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Project description:BackgroundThe highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to understand the mechanisms of virulence of this introduced pathogen and its evolving population structure, with a view to identifying potential strategies for the control of Dutch elm disease. As part of a larger study to examine the genomes of economically important Ophiostoma spp. and the genetic basis of virulence, we have constructed an expressed sequence tag (EST) library using total RNA extracted from the yeast-like growth phase of O. novo-ulmi (isolate H327).ResultsA total of 4,386 readable EST sequences were annotated by determining their closest matches to known or theoretical sequences in public databases by BLASTX analysis. Searches matched 2,093 sequences to entries found in Genbank, including 1,761 matches with known proteins and 332 matches with unknown (hypothetical/predicted) proteins. Known proteins included a collection of 880 unique transcripts which were categorized to obtain a functional profile of the transcriptome and to evaluate physiological function. These assignments yielded 20 primary functional categories (FunCat), the largest including Metabolism (FunCat 01, 20.28% of total), Sub-cellular localization (70, 10.23%), Protein synthesis (12, 10.14%), Transcription (11, 8.27%), Biogenesis of cellular components (42, 8.15%), Cellular transport, facilitation and routes (20, 6.08%), Classification unresolved (98, 5.80%), Cell rescue, defence and virulence (32, 5.31%) and the unclassified category, or known sequences of unknown metabolic function (99, 7.5%). A list of specific transcripts of interest was compiled to initiate an evaluation of their impact upon strain virulence in subsequent studies.ConclusionsThis is the first large-scale study of the O. novo-ulmi transcriptome. The expression profile obtained from the yeast-like growth phase of this species will facilitate a multigenic approach to gene expression studies to assess their role in the determination of pathogenicity for this species. The identification and evaluation of gene targets in such studies will be a prerequisite to the development of biological control strategies for this pathogen.

Dataset Information

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

Publications

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

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