Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

Abstract

BackgroundInappropriate 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.MethodologyHere, 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.ConclusionsA 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.

Evolution of pollen morphology in Loranthaceae

“…Data on Loranthaceae (in total 711 accessions) were harvested using the NCBI GenBank portal (accessed 3 April 2014) following the procedure outlined in Grimm and Renner (2013): GenBank flatfiles were read-out with gbk2fas (Göker et al 2009), data aligned using mafft (Katoh et al 2005; Katoh & Standley 2013) and visual inspections and curation of alignments done using Mesquite v. 2.75 (Maddison & Maddison 2011). The set-up and curation details can be found in File S2.…”

Mycorrhiza Networks Promote Biodiversity and Stabilize the Tropical Mountain Rain Forest Ecosystem: Perspectives for Understanding Complex Communities

“…Operational Taxonomic Units (OTUs) were defined as surrogates for species on the basis of sequence similarity by use of OPTSIL (Göker et al 2009) at <3 % divergence of ITS/5.8S sequences for Tulasnellales and Sebacinales and <1 % divergence of 18S for Glomeromycota. As delimitation of OTUs is still discussed (Hibbett et al 2011;Cruz et al 2011), we explored also delimitation of Tulasnellales at <5 % and Glomeromycota at <2 % divergence.…”

Canrightiopsis, a new Early Cretaceous fossil withClavatipollenites-type pollen bridge the gap between extinctCanrightiaand extant Chloranthaceae

“…NCBI GenBank flatfiles were read out using GBK2FAS (Göker et al 2009), alignment relied on MAFFT v7 (Katoh & Standley 2013), strictgenus consensus sequences were generated with G2CEF (Göker & Grimm 2008). RAXML v7.2.8 was used to find a topology with high likelihood and establish branch support via quick, non-parametric bootstrapping using a sufficient number of bootstrap replicates (Stamatakis 2006;Stamatakis et al 2008;Pattengale et al 2009 (Table I) follow Endress (2010, 2014) with a few exceptions.…”