Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.

<h4>Background</h4>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 or...

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Autores principales:	Markus Göker, Gema García-Blázquez, Hermann Voglmayr, M Teresa Tellería, María P Martín
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cd4d162de8b2499b9d9445012afa4653
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spelling	oai:doaj.org-article:cd4d162de8b2499b9d9445012afa46532021-11-25T06:21:22ZMolecular taxonomy of phytopathogenic fungi: a case study in Peronospora.1932-620310.1371/journal.pone.0006319https://doaj.org/article/cd4d162de8b2499b9d9445012afa46532009-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19641601/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology</h4>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.<h4>Conclusions</h4>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.Markus GökerGema García-BlázquezHermann VoglmayrM Teresa TelleríaMaría P MartínPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 7, p e6319 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Markus Göker Gema García-Blázquez Hermann Voglmayr M Teresa Tellería María P Martín Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
description	<h4>Background</h4>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.<h4>Methodology</h4>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.<h4>Conclusions</h4>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.
format	article
author	Markus Göker Gema García-Blázquez Hermann Voglmayr M Teresa Tellería María P Martín
author_facet	Markus Göker Gema García-Blázquez Hermann Voglmayr M Teresa Tellería María P Martín
author_sort	Markus Göker
title	Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
title_short	Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
title_full	Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
title_fullStr	Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
title_full_unstemmed	Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.
title_sort	molecular taxonomy of phytopathogenic fungi: a case study in peronospora.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/cd4d162de8b2499b9d9445012afa4653
work_keys_str_mv	AT markusgoker moleculartaxonomyofphytopathogenicfungiacasestudyinperonospora AT gemagarciablazquez moleculartaxonomyofphytopathogenicfungiacasestudyinperonospora AT hermannvoglmayr moleculartaxonomyofphytopathogenicfungiacasestudyinperonospora AT mteresatelleria moleculartaxonomyofphytopathogenicfungiacasestudyinperonospora AT mariapmartin moleculartaxonomyofphytopathogenicfungiacasestudyinperonospora
_version_	1718413827689676800

Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.

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