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Genomics data mining for the genetic analysis of populations of the Dutch elm disease (DED) fungi (Ophiostoma ulmi and O. novo-ulmi)

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Tools to identify genetic diversity

A European study investigated the existence of genetic diversity in the fungal pathogen Ophiostoma, which causes Dutch elm disease (DED).

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Ophiostoma has been accidentally introduced in Europe. The existence of inter-fertile Ophiostoma species and interspecies hybrids is feared to give rise to more pathogenic strains through gene flow. The EU-funded GENODED project aimed to identify new molecular markers for investigating the evolution of the Ophiostoma pathogen populations. To this end, the genome of the DED fungus was examined for simple sequence repeats or microsatellites — small stretches of DNA used for fingerprinting — and their polymorphisms. Specific polymerase chain reaction-based assays were developed for an array of these repeats. These were subsequently used to characterise fungal isolates from different sites in the Iberian Peninsula. Alongside these neutral microsatellites, genes of pathogenicity were also used as markers. Results indicated that in most locations differing Ophiostoma genotypes correlated to various levels of aggressiveness. The observed variability was attributed to sexual reproduction given that sexual spores were found to be the main spreading mechanism among elm trees. Specific polymorphisms associated with temperature tolerance were also detected. Additionally, the contribution of transposable elements to the observed genetic diversity was investigated. This was mainly applicable for polymorphisms generated in asexually-spread populations by the transposition of such elements within the genome. The GENODED analyses provided insight into the levels of gene flow and hybridisation among Ophiostoma populations. This information could form the basis for future studies on the evolutionary mechanisms that shape the populations of the DED fungi.

Keywords

Dutch elm disease, Ophiostoma, genetic diversity, sexual reproduction

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