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doi:10.5598/imafungus.2011.02.02.07 <strong>IMA</strong> <strong>Fungus</strong> · volume 2 · no 2: 163–171 The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora Fabian Runge 1 , Sabine Telle 2,3 , Sebastian Ploch 2,3 , Elizabeth Savory 4 , Brad Day 4 , Rahul Sharma 2,3,5 , and Marco Thines 2,3,5 1 University of Hohenheim, Institute of Botany 210, D-70593 Stuttgart, Germany 2 Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; corresponding author e-mail: marco.thines@senckenberg.de 3 Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany 4 Michigan State University, Department of Plant Pathology, 104 Center for Integrated Plant Systems, East Lansing, MI 48824, USA 5 Goethe University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, D-60323 Frankfurt (Main), Germany ARTICLE Abstract: Pathogens belonging to the Oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. In particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus Phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by P. ramorum, potato late blight caused by P. infestans, cucurbit downy mildew caused by Pseudoperonospora cubensis, and grape downy mildew caused by Plasmopara viticola. About 800 species of downy mildews and roughly 100 species of Phytophthora are currently accepted, and recent studies have revealed that these groups are closely related. However, the degree to which Phytophthora is paraphyletic and where exactly the downy mildews insert into this genus in relation to other clades could not be inferred with certainty to date. Here we present a molecular phylogeny encompassing all clades of Phytophthora as represented in a multilocus dataset and two representatives of the monophyletic downy mildews from divergent genera. Our results demonstrate that Phytophthora is at least six times paraphyletic with respect to the downy mildews. The downy mildew representatives are consistently nested within clade 4 (contains Phytophthora palmivora), which is placed sister to clade 1 (contains Phytophthora infestans). This finding would either necessitate placing all downy mildews and Phytopthora species in a single genus, either under the oldest generic name Peronospora or by conservation the later name Phytophthora, or the description of at least six new genera within Phytophthora. The complications of both options are discussed, and it is concluded that the latter is preferable, as it warrants fewer name changes and is more practical. Key words: AU test downy mildews multigene phylogeny Peronosporaceae Phytophthora taxonomy Article info: Submitted 21 September 2011; Accepted 20 October 2011; Published 11 November 2011. Introduction Oomycetes are a group of organisms that superficially resemble fungi in their hyphal growth and absorptive way of nutrition. However, they are not closely related to Mycota, but belong to a group of heterokont organisms, Straminipila (Dick 2001), which also includes diatoms and sea-weeds. Oomycetes have adapted to parasitism of plants at least three times, once in the Saprolegniales in the genera Aphanomyces and Pachymetra (Riethmüller et al. 1999, Diéguez-Uribeondo et al. 2009), and separately in Albuginales and Peronosporales (Riethmüller et al. 2002, Hudspeth et al. 2003, Thines et al. 2008). While the evolution of obligate biotrophy seems to be an ancient occurrence for the white blister rusts (Thines & Kamoun 2010), the downy mildews have more recently arisen from Phytophthora-like ancestors (Riethmüller et al. 2002, Göker et al. 2003, 2007, Thines et al. 2008, 2009, Thines 2009). The close relationship of the downy mildews and Phytophthora revealed by these studies is in contrast to the widely used taxonomic classifications of Waterhouse (1973) and Dick (1984, 2001), in which Phytophthora and Pythium were grouped together in the family Pythiaceae. Although Cooke et al. (2000) inferred a position of Peronospora sparsa as a sister group of clade 4 (as defined in that study) based on ITS sequences alone, no substantial phylogenetic resolution was present on the phylogenetic backbone, thus failing to position this group within the genus Phytophthora. Other studies (including multi-locus studies) that included both downy mildew and Phytophthora species have so far not resolved the placement of downy mildews in relation to the different clades of Phytophthora (Riethmüller et al. 2002, Göker et al. 2007, Thines et al. 2009, Giresse et al. 2010). Additionally, Thines et © 2011 International Mycological Association You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. volume 2 · no. 2 163
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