Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

Background: Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, d...

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Veröffentlicht in:	PloS one Jg. 4; H. 7; S. e6319
Hauptverfasser:	Göker, Markus, García-Blázquez, Gema, Voglmayr, Hermann, Tellería, M. Teresa, Martín, María P
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States Public Library of Science 29.07.2009 Public Library of Science (PLoS)
Schlagworte:	Algorithms Analysis Biodiversity Biological control Biological pest control Case reports Case studies classification Clustering Comparative studies Deoxyribonucleic acid Distributed processing Divergence DNA DNA sequencing DNA, Fungal Ecology/Community Ecology and Biodiversity Economic importance Eukaryotes Evolution Evolutionary Biology/Bioinformatics Fungi Gene sequencing Genetic divergence genetics internal transcribed spacers Likelihood Functions Microbiology/Plant-Biotic Interactions molecular operational taxonomic units molecular sequence data molecular systematics Morphology Nucleotide sequence nucleotide sequences Optimization Organisms Parasites Pathogens Peronospora Peronospora - classification Peronospora - genetics Peronospora farinosa Peronosporaceae Peronosporales Phylogenetics Phylogeny Physical characteristics Phytopathogenic fungi Plant Biology/Plant-Biotic Interactions plant pathogenic fungi Plant protection Plants (botany) Prokaryotes Pseudoperonospora Resampling ribosomal DNA Species Statistical methods Studies Taxa Taxonomy Trends
ISSN:	1932-6203, 1932-6203
Online-Zugang:	Volltext
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Zusammenfassung:	Background: Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Methodology: Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. Conclusions: A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.
Bibliographie:	http://dx.doi.org/10.1371/journal.pone.0006319 ObjectType-Case Study-2 SourceType-Scholarly Journals-1 content type line 14 ObjectType-Feature-4 ObjectType-Report-1 ObjectType-Article-3 ObjectType-Article-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: MG. Performed the experiments: GGB. Analyzed the data: MG HV. Contributed reagents/materials/analysis tools: MTT MPM. Wrote the paper: MG GGB MTT MPM HV.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0006319