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Molecular epidemiology of clonal lineages of an invasive fungal plant pathogen

English title Molecular epidemiology of clonal lineages of an invasive fungal plant pathogen
Applicant Prospero Simone
Number 170188
Funding scheme Project funding
Research institution Biodiversität und Naturschutzbiologie Eidg. Forschungsanstalt für Wald, Schnee und Landschaft WSL
Institution of higher education Swiss Federal Institute for Forest, Snow and Landscape Research - WSL
Main discipline Ecology
Start/End 01.01.2017 - 31.08.2020
Approved amount 230'008.00
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All Disciplines (3)

Discipline
Ecology
Environmental Research
Agricultural and Forestry Sciences

Keywords (5)

Biological invasions; Next generation sequencing; Population genomics; Ecological fitness; Asexual reproduction

Lay Summary (Italian)

Lead
La maggior parte dei funghi sono in grado di riprodursi sia sessualmente che asessualmente. Una predominanza della riproduzione asessuale (clonale) è frequente nei patogeni fungini invasivi all'inizio di un'epidemia. Nel corso del tempo, nuovi genotipi possono sorgere attraverso mutazioni e formare linee clonali persistenti e efficaci. Il progetto intende fornire un contributo ad una migliore comprensione di come queste linee clonali si diversificano nel tempo e nello spazio e del perché esse possono risultare così efficaci.
Lay summary

Soggetto e obiettivi

Recentemente l'avvento di nuove tecnologie di sequenziamento e un significativo progresso nelle tecniche di analisi dei dati hanno notevolmente aumentato le opportunità per la caratterizzazione genetica degli organismi clonali.

In questo progetto analizzeremo l'epidemiologia molecolare di linee clonali del fungo patogeno responsabile del cancro corticale del castagno (Cryphonectria parasitica). In particolare, ci concentreremo sulla linea clonale dominante nell’Europa sudorientale e su cloni in popolazioni svizzere. In una prima fase ricostruiremo la storia dell'invasione di C. parasitica nell’Europa sudorientale. In seguito determineremo perché un singolo clone di C. parasitica è diventato dominante in quella specifica regione. Infine indagheremo la diversificazione genetica nel tempo di cloni locali di C. parasitica. I nostri risultati contribuiranno in modo significativo a migliorare la comprensione scientifica dell’epidemiologia di linee clonali di organismi patogeni invasivi.

 

Contesto socio-scientifico

L’intensificazione degli scambi commerciali a livello mondiale e la maggiore mobilità delle persone sono alla base della crescente diffusione di specie invasive. Queste rappresentano una grande minaccia per la biodiversità, costituiscono un problema economico rilevante e possono pure risultare pericolose per la salute dell’uomo. Per poter sviluppare dei metodi di controllo efficaci, è perciò basilare capire come queste specie colonizzano i nuovi territori.

 

Direct link to Lay Summary Last update: 02.11.2016

Responsible applicant and co-applicants

Employees

Name Institute

Publications

Collaboration

Group / person Country
Types of collaboration
Faculty of Forestry, Chair for Protection of forests and wood, Skopje, Macedonia Macedonia (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Zagreb, Faculty of Science, Zagreb, Croatia Croatia (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Genetic Diversity Centre, ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Host-Microbes Genomics 2020 Talk given at a conference Lifestyle transitions in the genus Cryphonectria 11.09.2020 Birmensdorf, Switzerland Stauber Lea;
European Conference of Fungal Genetics ECFG15 Talk given at a conference Emergence and diversification of a highly invasive tree pathogen lineage 17.02.2020 Rome, Italy Stauber Lea;
Biology20 Poster Emergence and diversification of a highly invasive tree pathogen lineage 06.02.2020 Fribourg, Switzerland Stauber Lea;
Zurich Mycology Symposium 2020 Talk given at a conference Emergence and diversification of a highly invasive tree pathogen lineage 24.01.2020 Wädenswil, Switzerland Stauber Lea; Prospero Simone;
Host-Microbes Genomics 2019 Talk given at a conference Emergence and diversification of a highly invasive treepathogen lineage 24.09.2019 Zürich, Switzerland Stauber Lea; Prospero Simone;
IUFRO Phyllosphere Diseases Conference Talk given at a conference Molecular epidemiology of clonal lineages of an invasive fungal plant pathogen 05.05.2019 Florence, Italy Stauber Lea;
Host-Microbes Genomics 2017 Talk given at a conference Studying the invasion history of a widespread clonal chestnut blight (Cryphonectria parasitica) strain in south-eastern Europe 08.09.2017 Neuchâtel, Switzerland Stauber Lea; Prospero Simone;


Associated projects

Number Title Start Funding scheme
180651 Dynamics of virus infection in mycovirus-mediated biological control of a fungal pathogen 01.04.2019 Croatian-Swiss Research Programme (CSRP)

Abstract

Reproduction in fungi is complex and reflects the different life styles and genetic setup of these organisms. However, most fungi are able to undergo both asexual (clonal) and sexual reproduction. A predominance of asexual reproduction is frequently observed in invasive fungal plant pathogens at the beginning of an epidemic in a newly invaded area, when only one or a few genotypes of one mating type are present. Over time, in clonally reproducing genotypes novel genotypes may arise through mutations, resulting in clonal lineages. These may be highly successful, colonize large parts of the introduced range of the pathogen, and persist over years. In the last three decades, polymorphic molecular markers have been increasingly used to investigate amount and distribution of genetic variation in natural populations, with the assumption that such variation should reflect the main ecological important parameters. However, studies targeting asexual (clonal) organisms are still rare, most likely also because of the difficulties in detecting genetic variation within such organisms. Recently, the advent of so-called Next Generation Sequencing (NGS) technologies and significant progress in data analysis techniques have significantly increased the opportunities for genetic characterization of clonal organisms by allowing genome-scale analyses.In this project, we will investigate the molecular epidemiology of clonal lineages of the invasive pathogenic fungus Cryphonectria parasitica, the causal agent of chestnut blight. In particular, we will focus on the clonal lineage which is dominant in south-eastern Europe (from Croatia to western Turkey) and on local clones in Swiss populations. All these clones have been previously characterized using microsatellite markers. Here, we will (1) reconstruct the invasion history of C. parasitica in south-eastern Europe, (2) determine why a single clone of C. parasitica has become dominant in south-eastern Europe, and (3) investigate the genetic diversification over time in local clones of C. parasitica. For tasks (1) and (3) we will rely on genome-wide SNPs that we will detect by conducting whole-genome resequencing of a high number of isolates (600) from different geographic populations (task 1) and from sampling conducted at different times over a period of about 20 years (task 3). To reduce costs of sample preparation and sequencing we will adopt a low-coverage (7X) sequencing approach. In task 2, we will test two specific hypotheses, i.e. the “clonal selection” hypothesis (dominant clones have a greater fitness than rare genotypes) and the “first to come” hypothesis (clones become dominant only because of founder effects). Fitness of C. parasitica genotypes (the dominant clone in south-eastern Europe and two rare genotypes) will be quantified by assessing three phenotypic traits, namely virulence toward chestnut seedlings, growth on agar and on dormant chestnut stems, and sporulation on the cankers on the chestnut seedlings, on the dormant stems, and on agar. All inoculation will be performed in the biosafety greenhouse at WSL.Outcomes from this project will contribute significantly to improving scientific understanding of the epidemiology of clonal lineages of invasive pathogens. In particular, the project will shed light on the reasons why the invasive success of pathogenic fungi does not seem to be directly related to the genetic diversity and on the genetic evolution during establishment and subsequent range expansion.
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