GENODED · Genomics data mining for the genetic analysis of populations of the Dutch elm disease (DED) fungi (Ophiostoma ulmi and O. novo-ulmi)
FP7 — People (Marie Curie Actions)
- Duration
- 2009-11-01 → 2011-10-31
- EU contribution
- €198,267
- Participants
- 1
- Scheme
- MC-IOF
Lines connect the coordinator with its partners.
Results in brief
Genomics data mining for the genetic analysis of populations of the Dutch elm disease (DED) fungi (Ophiostoma ulmi and O. novo-ulmi)
Project context and objectives Two inter-fertile fungal species causing the Dutch elm disease (DED) (Ophiostoma ulmi and O. novo-ulmi) and two distinct subspecies of O. novo-ulmi, spp. novo-ulmi (European Access Network - EAN), and spp. americana (North American Network - NAN) coexist in elm stands in Europe, with interspecies and inter-subspecies hybrids. This constitutes an opportunity for a rapid emergence of new pathogenic races via inter-species/inter-subspecies gene flow. Work performed During the outgoing phase, in the partner organisation (Laval University, Canada), we developed new polymerase chain reaction (PCR)-based markers by mining Ophiostoma genomics data available at Dr Beniers' laboratory. We also used two main genetic resources: - ESTs (expressed sequences tags); - the sequence of the genome of the strain H327 of Ophiostoma novo-ulmi. During the return phase, in the Technical University of Madrid (Spain) we used such neutral (microsatellite deoxyribonucleic acid - DNA) and non-neutral molecular makers (genes of pathogenicity) to estimate the genetic diversity and genetic structure with various indexes of diversity and fixation, and allele frequency in both Mallorca and the Iberian Peninsula. We studied the transposable elements present in the strain H327, and characterised one copy and gypsy element in detail. We also studied the polymorphism of the gypsy element in O. ulmi and in both subspecies of Ophiostoma novo-ulmi, and their phylogenetic relationships. Main results Our data suggests that the sexual reproduction might have played a major role in the genetic diversity of current populations, since current natural populations of Ophiostoma in the Iberian Peninsula have sexual reproduction spread by sexual spores. The analyses provide an accurate idea of the levels of hybridisation and introgression, and the gene flow among populations. Our study provides new insights into the potential of transposable elements to generate genetic diversity by their activation. However, further studies will be necessary to discover the details of the evolutionary mechanisms that shape the populations of the DED fungi.
Data: CORDIS, © European Union
Project objective
RAPD analyses have shown that two inter-fertile fungal species causing the Dutch elm disease (DED) (Ophiostoma ulmi and O. novo-ulmi) coexist in elm stands in Europe, together with their interspecies hybrids. This constitutes an opportunity for a rapid emergence of new pathogenic races via interspecific gene flow. However, due to the drawbacks of the RAPD technique, new molecular markers should be designed to investigate the evolution of the pathogen populations. This project will enable the fellow to acquire the needed knowledge on the genomics of DED fungi to develop new molecular markers, in order to analyse the evolution of the populations of these pathogens in European elm stands. In the partner organization (Laval University, Canada), the fellow will develop the new markers by a mining of Ophiostoma genomics data obtained at this Canadian University. At Laval University the research program will include: (i) screening Ophiostoma ESTs libraries for microsatellites and PCR-RFLP; (ii) designing PCR-markers for several polymorphic fitness/pathogenic genes; and (iii) developing PCR-markers to detect genome changes generate by transposition of transposable elements (TEs). In the return institution (Polytechnic University of Madrid, Spain) the fellow will study the populations of the pathogens, and the evolutionary mechanisms that might lead the pathogens to overcome the elm resistance of breeding programs. The study of the populations will comprise: (iv) the levels of sexual reproduction, hybridisation and introgression; (v) the genetic structure and gene flow among populations; and (vi) the analysis of the polymorphism generated by TEs in order to investigate whether their activation increases the genetic diversity of the pathogen populations. Two potential evolutionary scenarios will be investigated: populations of the DED pathogens in equilibrium (sensitive elm stands), and under selection (tolerant elm stands).
Original text from CORDIS.
Participants
- UNIVERSIDAD POLITECNICA DE MADRID · MadridCoordinatorSpain
Links
Data: CORDIS, © European Union