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.
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Claims 12
Claim · model-written summary
Transcripts were identified for 6424 of 8640 annotated pathogen genes.
- Taxon
- American Elm
Ulmus americanat0 - Interactor
- O. novo-ulmiOphiostoma novo-ulmie0pathogen
- Outcome
- Transcripts were identified for 6424 of the 8640 protein-coding genes annotated in the O. novo-ulmi nuclear genomee0
- Value
- 6424 of the 8640 protein-coding genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“Transcripts were identified for 6424 of the 8640 protein-coding genes annotated in the O. novo-ulmi nuclear genome.”
Claim · model-written summary
1439 pathogen genes expressed in planta had PHI-base orthologs.
- Taxon
- American ElmUlmus americanat0
- Outcome
- genes expressed in planta had orthologs in the PHI-base curated databasee0
- Value
- 1439 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“A total of 1439 genes expressed in planta had orthologs in the PHI-base curated database of genes involved in host-pathogen interactions”
Claim · model-written summary
472 pathogen genes were differentially expressed at 96 hpi.
- Taxon
- American ElmUlmus americanat0
- Outcome
- genes were considered differentially expressede0
- Value
- 472 genese0
- Qualifier
- 96 hpie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“472 genes were considered differentially expressed (DEG) in S elms (370 genes) and VF elms (102 genes) at 96 hpi”
Claim · model-written summary
370 pathogen genes were differentially expressed in susceptible elms at 96 hpi.
- Taxon
- American ElmUlmus americanat0
- Outcome
- differentially expressed (DEG) in S elmse0
- Value
- 370 genese0
- Qualifier
- 96 hpie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“472 genes were considered differentially expressed (DEG) in S elms (370 genes) and VF elms (102 genes) at 96 hpi”
Claim · model-written summary
102 pathogen genes were differentially expressed in VF elms at 96 hpi.
- Taxon
- American ElmUlmus americanat0
- Outcome
- VF elmse0
- Value
- 102 genese0
- Qualifier
- 96 hpie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“472 genes were considered differentially expressed (DEG) in S elms (370 genes) and VF elms (102 genes) at 96 hpi”
Claim · model-written summary
Transport and transmembrane transport accounted for 27 of 55 enriched GO terms in genes upregulated in susceptible elms.
- Taxon
- American ElmUlmus americanat0
- Outcome
- GO terms that were significantly enriched in fungal genes upregulated in S elmse0
- Value
- 27/55e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“transport and transmembrane transport accounted for half (27/55) of GO terms that were significantly enriched in fungal genes upregulated in S elms”
Claim · model-written summary
Nine of 22 enriched GO terms in genes overexpressed in VF elms involved carbohydrate metabolism, catabolism or transport.
- Taxon
- American ElmUlmus americanat0
- Outcome
- GO terms associated with metabolism, catabolism and transport of carbohydratese0
- Value
- nine GO termse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“the 22 GO terms enriched in genes overexpressed in VF elms included nine GO terms associated with metabolism, catabolism and transport of carbohydrates”
Claim · model-written summary
Three coexpression modules were significantly associated with higher pathogen gene expression in susceptible elms.
- Taxon
- American ElmUlmus americanat0
- Material
- S elmse0
- Outcome
- gene expression in S elmse0
- Direction
- highere0
- Value
- three modulese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“three modules that were significantly associated with higher gene expression in S elms”
Claim · model-written summary
The three modules comprised 727 genes expressed in planta.
- Taxon
- American ElmUlmus americanat0
- Outcome
- genes expressed in plantae0
- Value
- 727 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“The three modules accounted for 727 genes expressed in planta”
Claim · model-written summary
The three modules included 103 genes upregulated in susceptible elms.
- Taxon
- American ElmUlmus americanat0
- Outcome
- DEGs upregulated in S elmse0
- Value
- 103 DEGse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“American Elm”
e0“included 103 DEGs upregulated in S elms”
Claim · model-written summary
Knockdown and knockout mutants of eight pathogen genes remained virulent toward elm saplings.
- Taxon
- U. americanaUlmus americanae0
- Treatment
- Knockdown- and knockout mutantse0
- Interactor
- O. novo-ulmiOphiostoma novo-ulmie0pathogen
- Outcome
- mutants remained virulent towards U. americana saplingse0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Knockdown- and knockout mutants were obtained for eight O. novo-ulmi genes. Although mutants remained virulent towards U. americana saplings”
Claim · model-written summary
The analysis identified additional candidate pathogen pathogenicity genes.
- Taxon
- O. novo-ulmiOphiostoma novo-ulmie0
- Outcome
- additional candidate O. novo-ulmi pathogenicity genese0
Verbatim
e0“we identified a large repertoire of additional candidate O. novo-ulmi pathogenicity genes for functional validation”