1
|
Koledenkova K, Esmaeel Q, Jacquard C, Nowak J, Clément C, Ait Barka E. Plasmopara viticola the Causal Agent of Downy Mildew of Grapevine: From Its Taxonomy to Disease Management. Front Microbiol 2022; 13:889472. [PMID: 35633680 PMCID: PMC9130769 DOI: 10.3389/fmicb.2022.889472] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/19/2022] [Indexed: 01/25/2023] Open
Abstract
Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni) causing grapevine downy mildew is one of the most damaging pathogens to viticulture worldwide. Since its recognition in the middle of nineteenth century, this disease has spread from America to Europe and then to all grapevine-growing countries, leading to significant economic losses due to the lack of efficient disease control. In 1885 copper was found to suppress many pathogens, and is still the most effective way to control downy mildews. During the twentieth century, contact and penetrating single-site fungicides have been developed for use against plant pathogens including downy mildews, but wide application has led to the appearance of pathogenic strains resistant to these treatments. Additionally, due to the negative environmental impact of chemical pesticides, the European Union restricted their use, triggering a rush to develop alternative tools such as resistant cultivars breeding, creation of new active ingredients, search for natural products and biocontrol agents that can be applied alone or in combination to kill the pathogen or mitigate its effect. This review summarizes data about the history, distribution, epidemiology, taxonomy, morphology, reproduction and infection mechanisms, symptoms, host-pathogen interactions, host resistance and control of the P. viticola, with a focus on sustainable methods, especially the use of biocontrol agents.
Collapse
Affiliation(s)
- Kseniia Koledenkova
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Jerzy Nowak
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Saunders Hall, Blacksburg, VA, United States
| | - Christophe Clément
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Essaid Ait Barka
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| |
Collapse
|
2
|
Crouch J, Davis W, Shishkoff N, Castroagudín V, Martin F, Michelmore R, Thines M. Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources. Fungal Syst Evol 2022; 9:43-86. [PMID: 35978987 PMCID: PMC9355112 DOI: 10.3114/fuse.2022.09.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/20/2022] [Indexed: 11/29/2022] Open
Abstract
Downy mildew pathogens of graminicolous hosts (Poaceae) are members of eight morphologically and phylogenetically distinct genera in the Peronosporaceae (Oomycota,Peronosporales). Graminicolous downy mildews (GDMs) cause severe losses in crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climates. In countries where the most destructive GDMs are not endemic, these organisms are often designated as high-risk foreign pathogens and subject to oversight and quarantine by regulatory officials. Thus, there is a need to reliably and accurately identify the causal organisms. This paper provides an overview of the Peronosporaceae species causing graminicolous downy mildew diseases, with a description of their impact on agriculture and the environment, along with brief summaries of the nomenclatural and taxonomic issues surrounding these taxa. Key diagnostic characters are summarized, including DNA sequence data for types and/or voucher specimens, morphological features, and new illustrations. New sequence data for cox2 and 28S rDNA markers are provided from the type specimens of three species, Peronosclerospora philippinensis, Sclerospora iseilematis, and Sclerospora northii. Thirty-nine species of graminicolous downy mildews are accepted, and seven previously invalidly published taxa are validated. Fifty-five specimens are formally designated as types, including lectotypification of 10 species, neotypification of three species, and holotype designation for Sclerophthora cryophila. Citation: Crouch JA, Davis WJ, Shishkoff N, Castroagudín VL, Martin F, Michelmore R, Thines M (2022). Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources. Fungal Systematics and Evolution9: 43–86. doi: 10.3114/fuse.2022.09.05
Collapse
Affiliation(s)
- J.A. Crouch
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
| | - W.J. Davis
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge Tennessee, USA
| | - N. Shishkoff
- USDA-ARS, Foreign Disease Weed Science Research Unit, Frederick, MD, USA
| | - V.L. Castroagudín
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge Tennessee, USA
| | - F. Martin
- USDA-ARS, Crop Improvement and Protection Research, Salinas, CA, USA
| | - R. Michelmore
- The Genome Center and Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - M. Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| |
Collapse
|
3
|
Buaya AT, Thines M. Miracula moenusica, a new member of the holocarpic parasitoid genus from the invasive freshwater diatom Pleurosira laevis. Fungal Syst Evol 2019; 3:35-40. [PMID: 32478313 PMCID: PMC7252423 DOI: 10.3114/fuse.2019.03.04] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Holocarpic oomycetes are poorly known but widespread parasites in freshwater and marine ecosystems. Most of the holocarpic species seem to belong to clades that diverge before the two crown lineages of the oomycetes, the Saprolegniomycetes and the Peronosporomycetes. Recently, the genus Miracula was described to accommodate Miracula helgolandica, a holocarpic parasitoid of Pseudo-nitzschia diatoms, which received varying support for its placement as the earliest-diverging oomycete lineage. In the same phylogenetic reconstruction, Miracula helgolandica was grouped with some somewhat divergent sequences derived from environmental sequencing, indicating that Miracula would not remain monotypic. Here, a second species of Miracula is reported, which was found as a parasitoid in the limnic centric diatom Pleurosira leavis. Its life-cycle stages are described and depicted in this study and its phylogenetic placement in the genus Miracula revealed. As a consequence, the newly discovered species is introduced as Miracula moenusica.
Collapse
Affiliation(s)
- A T Buaya
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60486 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - M Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60486 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| |
Collapse
|
4
|
Bennett RM, Devanadera MK, Dedeles GR. A revision of Salispina, its placement in a new family, Salispinaceae ( Rhipidiales), and description of a fourth species, S. hoi sp. nov. IMA Fungus 2018; 9:259-269. [PMID: 30622882 PMCID: PMC6317584 DOI: 10.5598/imafungus.2018.09.02.03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/17/2018] [Indexed: 01/24/2023] Open
Abstract
The genus Salispina was recently described for saprotrophic estuarine oomycetes with aculeolate or spiny sporangia. The genus currently contains three species, S. intermedia, S. lobata, and S. spinosa, the latter two previously included in Halophytophthora. During a survey of mangrove-inhabiting oomycetes in the Philippines, an isolate of Salispina (USTCMS 1611), was obtained from a decaying mangrove leaf. This isolate differed from other species in the genus in a unique combination of morphological and biological characters. Phylogenetic analysis revealed it to be the sister lineage of S. lobata. Consequently, the new species name S. hoi is introduced for the isolate. In addition, Salispina spp. grouped with Sapromyces of Rhipidiales with strong support, but differs from all other known genera of the order in the weak formation of hyphal constrictions, and absence of basal thalli and a holdfast network. The new family Salispinaceae is, therefore, described to accommodate Salispina in the order Rhipidiales.
Collapse
Affiliation(s)
- Reuel M Bennett
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | - Mark Kevin Devanadera
- Department of Biological Sciences-College of Science, Department of Biochemistry-Faculty of Pharmacy, and UST Collection of Microbial Strains (USTCMS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1015, Philippines
| | - Gina R Dedeles
- Department of Biological Sciences-College of Science, Department of Biochemistry-Faculty of Pharmacy, and UST Collection of Microbial Strains (USTCMS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1015, Philippines
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| |
Collapse
|
5
|
Bourret TB, Choudhury RA, Mehl HK, Blomquist CL, McRoberts N, Rizzo DM. Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora. PLoS One 2018. [PMID: 29529094 PMCID: PMC5846723 DOI: 10.1371/journal.pone.0192502] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.
Collapse
Affiliation(s)
- Tyler B. Bourret
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
- * E-mail:
| | - Robin A. Choudhury
- Plant Pathology Department, University of Florida, Gainesville, Florida, United States of America
| | - Heather K. Mehl
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - Cheryl L. Blomquist
- California Department of Food and Agriculture, Sacramento, California, United States of America
| | - Neil McRoberts
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - David M. Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| |
Collapse
|
6
|
Thines M, Telle S, Choi YJ, Tan YP, Shivas RG. Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews. IMA Fungus 2015; 6:483-91. [PMID: 26734551 PMCID: PMC4681264 DOI: 10.5598/imafungus.2015.06.02.12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/23/2015] [Indexed: 10/25/2022] Open
Abstract
So far 19 genera of downy mildews have been described, of which seven are parasitic to grasses. Here, we introduce a new genus, Baobabopsis, to accommodate two distinctive downy mildews, B. donbarrettii sp. nov., collected on Perotis rara in northern Australia, and B. enneapogonis sp. nov., collected on Enneapogon spp. in western and central Australia. Baobabopsis donbarrettii produced both oospores and sporangiospores that are morphologically distinct from other downy mildews on grasses. Molecular phylogenetic analyses showed that the two species of Baobabopsis occupied an isolated position among the known genera of graminicolous downy mildews. The importance of the Poaceae for the evolution of downy mildews is highlighted by the observation that more than a third of the known genera of downy mildews occur on grasses, while more than 90 % of the known species of downy mildews infect eudicots.
Collapse
Affiliation(s)
- Marco Thines
- Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany;; Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Senckenberg Gesellschaft für Naturkunde, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; Goethe University, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, May-von-Laue-Str. 9, D-60483 Frankfurt am Main, Germany
| | - Sabine Telle
- Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany;; Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | - Young-Joon Choi
- Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany;; Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Senckenberg Gesellschaft für Naturkunde, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Yu Pei Tan
- Plant Pathology Herbarium, Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, Qld 4001, Australia
| | - Roger G Shivas
- Plant Pathology Herbarium, Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, Qld 4001, Australia
| |
Collapse
|
7
|
A molecular phylogeny of Basidiophora reveals several apparently host-specific lineages on Astereae. Mycol Prog 2014. [DOI: 10.1007/s11557-014-1002-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
8
|
Göker M, Scheuner C, Klenk HP, Stielow JB, Menzel W. Codivergence of mycoviruses with their hosts. PLoS One 2011; 6:e22252. [PMID: 21829452 PMCID: PMC3146478 DOI: 10.1371/journal.pone.0022252] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/17/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The associations between pathogens and their hosts are complex and can result from any combination of evolutionary events such as codivergence, switching, and duplication of the pathogen. Mycoviruses are RNA viruses which infect fungi and for which natural vectors are so far unknown. Thus, lateral transfer might be improbable and codivergence their dominant mode of evolution. Accordingly, mycoviruses are a suitable target for statistical tests of virus-host codivergence, but inference of mycovirus phylogenies might be difficult because of low sequence similarity even within families. METHODOLOGY We analyzed here the evolutionary dynamics of all mycovirus families by comparing virus and host phylogenies. Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees. CONCLUSIONS While sequence alignment filtering modes affected branch support, the overall results of the co-phylogenetic tests were significantly influenced only by the number of viruses sampled per family. The trees of the two largest families, Partitiviridae and Totiviridae, were significantly more similar to those of their hosts than expected by chance, and most individual host-virus links had a significant positive impact on the global fit, indicating that codivergence is the dominant mode of virus diversification. However, in this regard mycoviruses did not differ from closely related viruses sampled from non-fungus hosts. The remaining virus families were either dominated by other evolutionary modes or lacked an apparent overall pattern. As this negative result might be caused by insufficient taxon sampling, the most parsimonious hypothesis still is that host-parasite evolution is basically the same in all mycovirus families. This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range itself.
Collapse
Affiliation(s)
- Markus Göker
- DSMZ-German Collection for Microorganisms and Cell Cultures, Braunschweig, Germany.
| | | | | | | | | |
Collapse
|
9
|
Hybrid genera in Liatrinae (Asteraceae: Eupatorieae). Mol Phylogenet Evol 2011; 59:158-67. [DOI: 10.1016/j.ympev.2011.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 11/21/2022]
|
10
|
Reclassification of an enigmatic downy mildew species on lovegrass (Eragrostis) to the new genus Eraphthora, with a key to the genera of the Peronosporaceae. Mycol Prog 2011. [DOI: 10.1007/s11557-010-0735-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Salisapiliaceae - a new family of oomycetes from marsh grass litter of southeastern North America. Persoonia - Molecular Phylogeny and Evolution of Fungi 2010; 25:109-16. [PMID: 21339970 PMCID: PMC3028510 DOI: 10.3767/003158510x551763] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 10/26/2010] [Indexed: 11/25/2022]
Abstract
Several filamentous oomycete species of the genus Halophytophthora have recently been described from marine environments, mostly from subtropical and tropical ecosystems. During a survey of oomycetes from leaf litter of Spartina alterniflora in salt marshes of southeastern Georgia, isolates of four taxa were recovered that bore similarity to some members of Halophytophthora but were highly divergent from isolates of Halophytophthora s.str. based on a combined sequence analysis of two nuclear loci. In phylogenetic analyses, these isolates were placed basal to a monophyletic group comprised of Pythium of the Pythiaceae and the Peronosporaceae. Sequence and morphology of these taxa diverged from the type species Halophytophthora vesicula, which was placed within the Peronosporaceae with maximum support. As a consequence a new family, the Salisapiliaceae, and a new genus, Salisapilia, are described to accommodate the newly discovered species, along with one species previously classified within Halophytophthora. Morphological features that separate these taxa from Halophytophthora are a smaller hyphal diameter, oospore production, lack of vesicle formation during sporulation, and a plug of hyaline material at the sporangial apex that is displaced during zoospore release. Our findings offer a first glance at the presumably much higher diversity of oomycetes in estuarine environments, of which ecological significance requires further exploration.
Collapse
|
12
|
Evidence for high degrees of specialisation, evolutionary diversity, and morphological distinctiveness in the genus Bremia. Fungal Biol 2010; 115:102-11. [PMID: 21315308 DOI: 10.1016/j.funbio.2010.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 10/16/2010] [Accepted: 10/27/2010] [Indexed: 11/21/2022]
Abstract
Bremia lactucae is one of the most important pathogens in lettuce production. Recent molecular studies revealed considerable genetic variation in this species complex. However, only few accessions from the same host have been examined for most species and no study investigating the morphological distinctiveness of phylogenetic lineages of Bremia has so far been reported. Thus it is believed that morphological species delimitation in Bremia is not feasible. In the present study, multiple accessions of neglected species, which had been described decades ago, but have not been widely accepted, were investigated, considering both multi-gene phylogenies and morphological characters. All previously described species from host genera other than Lactuca investigated, Bremia microspora, Bremia ovata, Bremia saussureae, and Bremia sonchicola, could be confirmed as distinct, host-specific entities. Also, morphological characteristics of their conidiophores and conidia allowed delimitation of these species. Therefore, not only the wide species concept to merge all Bremia species on the Asteraceae under B. lactucae is inappropriate but also their delimitation on the basis of morphological characters seems feasible. In addition, it has been shown that Bremia elliptica is phylogenetically distinct from the other species infecting the genus Lactuca, B. lactucae. It is therefore concluded that B. lactucae is most likely limited to Lactuca sativa and closely-related species, and that most species of Bremia are highly host specific. This finding might stimulate the search for durable resistance genes in genera closely related to the genus Lactuca and in divergent species of the genus itself.
Collapse
|
13
|
Thines M. Bridging the gulf: Phytophthora and downy mildews are connected by rare grass parasites. PLoS One 2009; 4:e4790. [PMID: 19274081 PMCID: PMC2651470 DOI: 10.1371/journal.pone.0004790] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Accepted: 07/28/2008] [Indexed: 11/19/2022] Open
Abstract
Downy mildews and root and foliar rots caused by Phytophthora are among the most destructive plant pathogens and therefore have attracted considerable attention during the past two decades. Although it has been realized that a close phylogenetic relationship exists, so far sharp distinction has been made between the obligate biotrophic downy mildews and the hemibiotrophic Phytophthora. In the study presented here, it is shown that a continuum of character states from hemibiotrophic Phytophthora species to obligate biotrophic downy mildews is present. Intermediate character states between downy mildews and Phytophthora species exist in several rare parasites of grasses, which are not embedded within the major clades of the downy mildews but are placed sister to these, with unresolved affinities to both these clades and to Phytophthora. They still have retained traits hitherto thought to be exclusive for Phytophthora. A careful review of previous research is presented and it is highlighted that uniquely for downy mildews, Poakatesthia may form an intracellular mycelium, growing through several host cells. In addition, scanning electron microscopy reveals that sporangiophore growth is not determinate in Viennotia and that outgrowth from sporangiophores is very similar to Phytophthora infestans. It is concluded that the sharp morphological distinction between downy mildews and Phytophthora species (that are often placed in separate families and even different orders), is rather artificial, since all features thought to be exclusive to Phytophthora or the downy mildews are united in the rare grass-parasitizing down mildew genera Viennotia and Poakatesthia and the enigmatic genus Sclerophthora. Therefore, several paradigms regarding the distinction between Phytophthora and the downy mildews need to be reconsidered.
Collapse
Affiliation(s)
- Marco Thines
- Institute of Botany, University of Hohenheim, Stuttgart, Germany.
| |
Collapse
|
14
|
García-Blázquez G, Göker M, Voglmayr H, Martín MP, Tellería MT, Oberwinkler F. Phylogeny of Peronospora, parasitic on Fabaceae, based on ITS sequences. ACTA ACUST UNITED AC 2007; 112:502-12. [PMID: 18406121 DOI: 10.1016/j.mycres.2007.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 08/23/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
Abstract
Species concepts are a notoriously difficult taxonomic problem in plant-parasitic fungal-like organisms such as downy mildews (Peronosporomycetes, Peronosporales). This is particularly evident in the largest downy mildew genus, Peronospora, which contains a number of economically important pathogens. Here, we investigate relationships of Peronospora species infecting Fabaceae (angiosperms, Rosidae) originating from various collections from different species of host plants and from different European locations by molecular phylogenetic analysis of ITS sequences. Molecular trees were inferred with ML, MP and Bayesian methods and rooted with Pseudoperonospora. As in other downy mildew groups, molecular data mainly support the use of narrow species delimitations and host range as a taxonomic marker. Fabaceae parasites appear to be subdivided into a number of lineages displaying a considerable degree of host specialization with respect to host genera, as well as host subgenera or species. The number of repeats of a repetitive part of the ITS1 is, within limits, characteristic of subgroups within the cluster of Trifolium parasites. We reveal new hosts for Peronospora found on the Iberian Peninsula.
Collapse
Affiliation(s)
- Gema García-Blázquez
- Departamento de Micología, Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
15
|
Thines M, Göker M, Telle S, Ryley M, Mathur K, Narayana YD, Spring O, Thakur RP. Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data. ACTA ACUST UNITED AC 2007; 112:345-51. [PMID: 18308532 DOI: 10.1016/j.mycres.2007.10.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 09/03/2007] [Accepted: 10/23/2007] [Indexed: 11/17/2022]
Abstract
Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.
Collapse
Affiliation(s)
- Marco Thines
- Universität Hohenheim, Institut für Botanik, Garbenstr. 30, 70599 Stuttgart, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Thines M, Göker M, Oberwinkler F, Spring O. A revision of Plasmopara penniseti, with implications for the host range of the downy mildews with pyriform haustoria. ACTA ACUST UNITED AC 2007; 111:1377-85. [PMID: 18023988 DOI: 10.1016/j.mycres.2007.09.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 08/09/2007] [Accepted: 09/20/2007] [Indexed: 11/29/2022]
Abstract
Plasmopara penniseti is the sole member of the genus Plasmopara parasitic to Poaceae, after the genus Viennotia had been described to accommodate Plasmopara oplismeni. Morphological, ultrastructural, and molecular phylogenetic data indicate that Plasmopara penniseti is not closely related to the generic type, and it is, therefore, transferred to the newly described genus Poakatesthia. The view that the genera of downy mildews with pyriform to vesicular haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, and Protobremia) include species parasitic to Poaceae has to be discarded. All of these genera are apparently restricted to dicotyledonous hosts.
Collapse
Affiliation(s)
- Marco Thines
- University of Hohenheim, Institute of Botany 210, Garbenstr. 30, 70599 Stuttgart, Germany.
| | | | | | | |
Collapse
|
17
|
Göker M, Voglmayr H, Riethmüller A, Oberwinkler F. How do obligate parasites evolve? A multi-gene phylogenetic analysis of downy mildews. Fungal Genet Biol 2006; 44:105-22. [PMID: 16990040 DOI: 10.1016/j.fgb.2006.07.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 07/14/2006] [Accepted: 07/19/2006] [Indexed: 10/24/2022]
Abstract
Plant parasitism has independently evolved as a nutrition strategy in both true fungi and Oomycetes (stramenopiles). A large number of species within phytopathogenic Oomycetes, the so-called downy mildews, are defined as obligate biotrophs since they have not, to date, been cultured on any artificial medium. Other genera like Phytophthora and Pythium can in general be cultured on standard or non-standard agar media. Within all three groups there are many important plant pathogens responsible for severe economic losses as well as damage to natural ecosystems. Although they are important model systems to elucidate the evolution of obligate parasites, the phylogenetic relationships between these genera have not been clearly resolved. Based on the most comprehensive sampling of downy mildew genera to date and a representative sample of Phytophthora subgroups, we inferred the phylogenetic relationships from a multi-gene dataset containing both coding and non-coding nuclear and mitochondrial loci. Phylogenetic analyses were conducted under several optimality criteria and the results were largely consistent between all the methods applied. Strong support is achieved for monophyly of a clade comprising both the genus Phytophthora and the obligate biotrophic species. The facultatively parasitic genus Phytophthora is shown to be at least partly paraphyletic. Monophyly of a cluster nested within Phytophthora containing all obligate parasites is strongly supported. Within the obligate biotrophic downy mildews, four morphologically or ecologically well-defined subgroups receive statistical support: (1) A cluster containing all species with brownish-violet conidiosporangia, i.e., the genera Peronospora and Pseudoperonospora; (2) a clade comprising the genera with vesicular to pyriform haustoria (Basidiophora, Benua, Bremia, Paraperonospora, Plasmopara, Plasmoverna, Protobremia); (3) a group containing species included in Hyaloperonospora and Perofascia which almost exclusively infect Brassicaceae; (4) a clade including the grass parasites Viennotia oplismeni and Graminivora graminicola. Phylogenetic relationships between these four clades are not clearly resolved, and neither is the position of Sclerospora graminicola within the downy mildews. Character analysis indicates an evolutionary scenario of gradually increasing adaptation to plant parasitism in Peronosporales and that at least the most important of these adaptive steps occurred only once, including major host shifts within downy mildews.
Collapse
Affiliation(s)
- Markus Göker
- Lehrstuhl für Spezielle Botanik und Mykologie, Botanisches Institut, Universität Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany.
| | | | | | | |
Collapse
|
18
|
Auch AF, Henz SR, Holland BR, Göker M. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics 2006; 7:350. [PMID: 16854218 PMCID: PMC1564419 DOI: 10.1186/1471-2105-7-350] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 07/19/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called delta value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. delta values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION Using the most treelike distance matrices, as judged by their delta values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. delta values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference.
Collapse
Affiliation(s)
- Alexander F Auch
- Center for Bioinformatics (ZBIT), Sand 14, Tübingen, University of Tübingen, Germany
| | - Stefan R Henz
- Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, Tübingen, Germany
| | - Barbara R Holland
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
| | - Markus Göker
- Organismic Botany/Mycology, Auf der Morgenstelle 1, Tübingen, University of Tübingen, Germany
| |
Collapse
|