Genomics of the Dutch elm disease pathosystem: are we there yet?

Bernier, Louis; Aoun, Mirella; Bouvet, Guillaume F.; Comeau, A.; Dufour, J.; Naruzawa, Erika Sayuri; Nigg, Martha; Plourde, Karine V.

doi:10.3832/ifor1211-008

Cited by 18 publications

(14 citation statements)

References 95 publications

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“…O. novo-ulmi is a model species in terms of its interaction with the host tree, its epidemiology, and its high virulence. This fungus has been studied for many years with respect to its involvement in Dutch elm disease ( Bernier et al 2015 ). As is the case with many other dimorphic fungi, this pathogen is capable of living either in a yeast phase or in a mycelial phase, depending on environmental conditions.…”

Section: Resultsmentioning

confidence: 99%

“…Both phases seem to be required to insure the complete infection of elm trees ( Miller and Elgersma 1976 ). The nuclear genome of O. novo-ulmi was recently sequenced ( Forgetta et al 2013 ; Bernier et al 2015 ) and contains approximately 8640 coding genes, of which approximately 25% remain unannotated ( Comeau et al 2015 ). Knowing which of these genes are expressed specifically in the yeast and mycelium phases remains undetermined because data for O. novo-ulmi consist largely of expressed sequence tags (ESTs) that are associated with the yeast phase ( Hintz et al 2011 ) and the production of fruiting bodies ( Jacobi et al 2010 ).…”

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confidence: 99%

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RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease FungusOphiostoma novo-ulmi

Nigg

Laroche

Landry

et al. 2015

G3 Genes|Genomes|Genetics

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Fungal dimorphism is a complex trait and our understanding of the ability of fungi to display different growth morphologies is limited to a small number of model species. Here we study a highly aggressive dimorphic fungus, the ascomycete Ophiostoma novo-ulmi, which is a model in plant pathology and the causal agent of Dutch elm disease. The two growth phases that this fungus displays, i.e., a yeast phase and mycelial phase, are thought to be involved in key steps of disease development. We used RNAseq to investigate the genome-wide gene expression profiles that are associated with yeast and mycelial growth phases in vitro. Our results show a clear molecular distinction between yeast and mycelial phase gene expression profiles. Almost 12% of the gene content is differentially expressed between the two phases, which reveals specific functions related to each growth phase. We compared O. novo-ulmi transcriptome profiles with those of two model dimorphic fungi, Candida albicans and Histoplasma capsulatum. Few orthologs showed similar expression regulation between the two growth phases, which suggests that, globally, the genes associated with these two life forms are poorly conserved. This poor conservation underscores the importance of developing specific tools for emerging model species that are distantly related to the classical ones. Taken together, our results provide insights into transcriptome regulation and molecular specificity in O. novo-ulmi and offer a new perspective for understanding fungal dimorphism.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease FungusOphiostoma novo-ulmi

Nigg

Laroche

Landry

et al. 2015

G3 Genes|Genomes|Genetics

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“…; Bernier et al. ). Molecules secreted by the fungus also enhance xylem vulnerability to cavitation by reducing the sap surface tension and by degrading intervessel pit membranes (Newbanks et al.…”

Section: Introductionmentioning

confidence: 97%

Physiological and biochemical differences amongUlmus minorgenotypes showing a gradient of resistance toDutch elm disease

López

Venturas

et al. 2015

Forest Pathology

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Dutch elm disease (DED) spread across Europe and North America in the 20th century killing most natural elm populations. Today, breeding programmes aim at identifying, propagating and studying elm clones resistant to DED. Here, we have compared the physiology and biochemistry of six genotypes of Ulmus minor of variable DED resistance. Leaf gas exchange, water potential, stem hydraulic conductivity and biochemical status were studied in 5-year-old trees of AB-AM2.4, M-DV2.3, M-DV2 9 M-CC1.5 and M-DV1 and 6-year-old trees of VA-AP38 and BU-FL7 before and after inoculation with Ophiostoma novo-ulmi. Leaf water potential and net photosynthesis rates declined, while the percentage loss of hydraulic conductivity (PLC) increased after the inoculation in susceptible trees. By the 21st day, leaf predawn and midday water potential, stomatal conductance to water vapour and net photosynthesis rates were lower, and PLC was higher in trees of susceptible (S) genotypes inoculated with the pathogen than in control trees inoculated with water, whereas no significant treatment effect was observed on these variables in the resistant (R) genotypes. Fourier transform infrared spectroscopy analyses revealed a different biochemical profile for branches of R and S clones. R clones showed higher absorption peaks that could be assigned to phenolic compounds, saturated hydrocarbons, cellulose and hemicellulose than S clones. The differences were more marked at the end of the experiment than at the beginning, suggesting that R and S clones responded differently to the inevitable wounding from inoculation and repeated sampling over the experimental course. We hypothesize that a weak activation of the defence system in response to experimental wounding can contribute to the susceptibility of some genotypes to O. novo-ulmi. In turn, the decline in shoot hydraulic conductivity and leaf carbon uptake caused by the infection further exacerbates tree susceptibility to the fungus.

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“…The available Ulmus sp. molecular resources are clearly insufficient to preserve and manage the threatened elm populations ( Bernier et al, 2015 ). Large-scale development of SNP markers would allow researchers to use more efficient and powerful tools in the management and conservation of U. minor genetic resources and those of other Ulmaceae species.…”

Section: Introductionmentioning

confidence: 99%

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

et al. 2015

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Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.

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Genomics of the Dutch elm disease pathosystem: are we there yet?

Cited by 18 publications

References 95 publications

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease FungusOphiostoma novo-ulmi

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease FungusOphiostoma novo-ulmi

Physiological and biochemical differences amongUlmus minorgenotypes showing a gradient of resistance toDutch elm disease

Massive sequencing of Ulmus minor’s transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

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