Abstract
BackgroundMolecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Åland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001.Principal FindingsA cDNA library of a pooled sample of fungal conidia was sequenced on the 454 GS-FLX platform. Over 549,411 reads were obtained and annotated into 45,245 contigs. Annotation data was acquired for 65.2% of the assembled sequences. The transcriptome assembly was screened for SNP loci, as well as for functionally important genes (mating-type genes and potential effector proteins). A genotyping assay of 27 SNP loci was designed and tested on 380 infected leaf samples from 80 populations within the Åland archipelago. With this panel we identified 85 multilocus genotypes (MLG) with uneven frequencies across the pathogen metapopulation. Approximately half of the sampled populations contain polymorphism. Our genotyping protocol revealed mixed-genotype infection within a single host leaf to be common. Mixed infection has been proposed as one of the main drivers of pathogen evolution, and hence may be an important process in this pathosystem.SignificanceThe developed SNP panel offers exciting research perspectives for future studies in this well-characterized pathosystem. Also, the transcriptome provides an invaluable novel genomic resource for powdery mildews, which cause significant yield losses on commercially important crops annually. Furthermore, the features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and hence our results provide methodological insights from SNP calling to field sampling protocols for a wide range of biological systems.
Highlights
Molecular tools in parasite species can address a range of exciting questions both from evolutionary and ecological perspectives [1]
The features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and our results provide methodological insights from Single Nucleotide Polymorphism (SNP) calling to field sampling protocols for a wide range of biological systems
The SNP array designed in this study would mostly be relevant to Po. plantaginis in the Aland archipelago because of ascertainment bias and lack of cross-amplification [29], we describe here some functionally important genes such as mating-type genes and candidate effectors
Summary
The occurrence of this pathogen has been intensively studied since 2001 in the Aland archipelago, south-west Finland, with more than 4,000 host plant populations surveyed each year by 40–70 students recording the presenceabsence of the pathogen (for details on the large-scale survey, see [4]). Molecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Aland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001
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