1 research outputs found
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, 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.Peer reviewe