An expanded phylogeny for the genus  Phytophthora

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Abstract

A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

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Most cited references 152

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Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

Brett M Tyler, Sucheta Tripathy, Xuemin Zhang … (2006)

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

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A molecular phylogeny of Phytophthora and related oomycetes.

D.E.L. Cooke, A Drenth, J.M. Duncan … (2000)

Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phytophthora was essentially monophyletic, all but three species forming a cluster of eight clades. Two clades contained only species with nonpapillate sporangia. The other six clades included either papillate and semipapillate, or semipapillate and nonpapillate types, transcending traditional morphological groupings, which are evidently not natural assemblages. Peronospora was related to P. megakarya and P. palmivora and appears to be derived from a Phytophthora that has both lost the ability to produce zoospores and become an obligate biotroph. Three other Phytophthoras located some distance from the main Phytophthora-Peronospora cluster probably represent one or more additional genera.

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A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences.

Jaime E Blair, Michael Coffey, Sook-Young Park … (2008)

Phytophthora species are devastating plant pathogens in both agricultural and natural environments. Due to their significant economic and environmental impact, there has been increasing interest in Phytophthora genetics and genomics, culminating in the recent release of three complete genome sequences (P. ramorum, P. sojae, and P. infestans). In this study, genome and other large sequence databases were used to identify over 225 potential genetic markers for phylogenetic analyses. Here, we present a genus-wide phylogeny for 82 Phytophthora species using seven of the most informative loci (approximately 8700 nucleotide sites). Our results support the division of the genus into 10 well-supported clades. The relationships among these clades were rigorously evaluated using a number of phylogenetic methods. This is the most comprehensive study of Phytophthora relationships to date, and many newly discovered species have been included. A more resolved phylogeny of Phytophthora species will allow for better interpretations of the overall evolutionary history of the genus.

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Author and article information

Journal

Journal ID (nlm-ta): IMA Fungus

Journal ID (iso-abbrev): IMA Fungus

Journal ID (publisher-id): IMA Fungus

Title: IMA Fungus

Publisher: International Mycological Association

ISSN (Print): 2210-6340

ISSN (Electronic): 2210-6359

Publication date (Electronic): 21 November 2017

Publication date (Print): December 2017

Volume: 8

Issue: 2

Pages: 355-384

Affiliations

[1 ]Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA;

[2 ]Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA

Author notes

corresponding author e-mail: yxiao9@ 123456vt.edu

Article

DOI: 10.5598/imafungus.2017.08.02.09

PMC ID: 5729717

PubMed ID: 29242780

SO-VID: c3efa796-0cfe-43b4-9c3f-d63daf16d13b

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An expanded phylogeny for the genus Phytophthora

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Abstract

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Crocodylian evolution

Most cited references 152

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

A molecular phylogeny of Phytophthora and related oomycetes.

A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences.

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