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Ploch S, Kruse J, Choi YJ, Thiel H, Thines M. Ancestral state reconstruction in Peronospora provides further evidence for host jumping as a key element in the diversification of obligate parasites. Mol Phylogenet Evol 2021; 166:107321. [PMID: 34626809 DOI: 10.1016/j.ympev.2021.107321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/08/2021] [Accepted: 10/04/2021] [Indexed: 11/15/2022]
Abstract
Biotrophic plant parasites cause economically important diseases, e.g. downy mildew of grape, powdery mildew of legumes, wheat stripe rust, and wheat bunt. But also in natural ecosystems, these organisms are abundant and diverse, and for many hosts more than one specialised biotrophic pathogen is known. However, only a fraction of their diversity is thought to have been described. There is accumulating evidence for the importance of host jumping for the diversification of obligate biotrophic pathogens but tracing this process along the phylogeny of pathogens is often complicated by a lack of resolution of phylogenetic trees, low taxon and specimen sampling, or either too few or too many host jumps in the pathogen group in question. Here, a clade of Peronospora species mostly infecting members of the Ranunculales was investigated using multigene analyses and ancestral state reconstructions. These analyses show that this clade started out in Papaveraceae, with subsequent host jumps to Berberidaceae, Euphorbiaceae, and Ranunculaceae. In Ranunculaceae, radiation to a variety of hosts took place, and a new host jump occurred to Caryophyllaceae. This highlights that host jumping and subsequent radiation is a key evolutionary process driving the diversification of Peronospora. It seems likely that the observed pattern can be generalised to other obligate parasite lineages, as diverse hosts in unrelated families have also been reported for other pathogen groups, including powdery mildew, rust fungi, and smut fungi.
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Affiliation(s)
- Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
| | - Julia Kruse
- Pfalzmuseum für Naturkunde - POLLICHIA-Museum, Hermann-Schäfer-Str. 17, 67098 Bad Dürkheim, Germany
| | - Young-Joon Choi
- Department of Biology, College of Natural Sciences, Kunsan National University, Gunsan 54150, Republic of Korea
| | | | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
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2
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Mirzaee MR, Ploch S, Thines M. A new desert-dwelling oomycete, Pustula persica sp. nov., on Gymnarrhena micrantha ( Asteraceae) from Iran. MYCOSCIENCE 2021; 62:239-243. [PMID: 37092169 PMCID: PMC9721518 DOI: 10.47371/mycosci.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
The obligate biotrophic oomycete genus Pustula is one of the four major linages of white blister rusts (Albuginaceae) identified so far. Species of the genus Pustula cause white blister rust on numerous genera in the asterids, represented by several phylogenetically distinct genus-specific lineages, most of which still await formal description. Thus, the observation of the species of Pustula on the Asteraceae subfamily Gymnorhenoideae pointed out to the existence of a hitherto undescribed species. By the morphological and molecular phylogenetic investigation conducted in this study it is concluded that the pathogen on Gymnarrhena micrantha from Iran indeed represents a hitherto unknown species and is described as P. persica. This species has apparently adapted to desert condition and is, after Albugo arenosa, the second species of white blister rust from Iranian deserts, highlighting the adaptability of white blister rusts to hot and dry habitats.
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Affiliation(s)
- Mohammad Reza Mirzaee
- Plant Protection Research Department, South Khorasan Agricultural and Natural Resources Research and Education Center, AREEO
| | | | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre
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3
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Sapp M, Tyborski N, Linstädter A, López Sánchez A, Mansfeldt T, Waldhoff G, Bareth G, Bonkowski M, Rose LE. Site-specific distribution of oak rhizosphere-associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding. Ecol Evol 2019; 9:10567-10581. [PMID: 31624568 PMCID: PMC6787841 DOI: 10.1002/ece3.5577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/19/2023] Open
Abstract
The phylum Oomycota comprises important tree pathogens like Phytophthora quercina, involved in central European oak decline, and Phytophthora cinnamomi shown to affect holm oaks among many other hosts. Despite the importance to study the distribution, dispersal and niche partitioning of this phylum, metabarcoding surveys, and studies considering environmental factors that could explain oomycete community patterns are still rare. We investigated oomycetes in the rhizosphere of evergreen oaks in a Spanish oak woodland using metabarcoding based on Illumina sequencing of the taxonomic marker cytochrome c oxidase subunit II (cox2). We developed an approach amplifying a 333 bp long fragment using the forward primer Hud-F (Mycologia, 2000) and a reverse primer found using DegePrime (Applied and Environmental Microbiology, 2014). Factors reflecting topo-edaphic conditions and tree health were linked to oomycete community patterns. The majority of detected OTUs belonged to the Peronosporales. Most taxa were relatives of the Pythiaceae, but relatives of the Peronosporaceae and members of the Saprolegniales were also found. The most abundant OTUs were related to Globisporangium irregulare and P. cinnamomi, both displaying strong site-specific patterns. Oomycete communities were strongly correlated with the environmental factors: altitude, crown foliation, slope and soil skeleton and soil nitrogen. Our findings illustrate the significance of small scale variation in habitat conditions for the distribution of oomycetes and highlight the importance to study oomycete communities in relation to such ecological patterns.
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Affiliation(s)
- Melanie Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS)Population GeneticsHeinrich Heine UniversityDüsseldorfGermany
| | - Nicolas Tyborski
- Cluster of Excellence on Plant Sciences (CEPLAS)Population GeneticsHeinrich Heine UniversityDüsseldorfGermany
| | - Anja Linstädter
- Botanical Institute, Range Ecology and Range ManagementUniversity of CologneCologneGermany
- Institute of Crop Science and Resource Conservation (INRES)University of BonnBonnGermany
| | - Aida López Sánchez
- Botanical Institute, Range Ecology and Range ManagementUniversity of CologneCologneGermany
- Departamento de Sistemas y Recursos NaturalesUniversidad Politécnica de MadridMadridSpain
| | - Tim Mansfeldt
- Institute of GeographyUniversity of CologneCologneGermany
| | - Guido Waldhoff
- Institute of GeographyUniversity of CologneCologneGermany
| | - Georg Bareth
- Institute of GeographyUniversity of CologneCologneGermany
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS)Institute of ZoologyTerrestrial EcologyUniversity of CologneCologneGermany
| | - Laura E. Rose
- Cluster of Excellence on Plant Sciences (CEPLAS)Population GeneticsHeinrich Heine UniversityDüsseldorfGermany
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Xu B, Choi YJ, Song JG, Zhang SH, Xi PG, Shin HD, De Jiang Z. Two new species of Pustula (Albuginales, Oomycota) from Junggar Basin in China based on morphology and molecular data. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1378-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kruse J, Dietrich W, Zimmermann H, Klenke F, Richter U, Richter H, Thines M. Ustilago species causing leaf-stripe smut revisited. IMA Fungus 2018; 9:49-73. [PMID: 30018872 PMCID: PMC6048562 DOI: 10.5598/imafungus.2018.09.01.05] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/12/2018] [Indexed: 12/02/2022] Open
Abstract
Leaf-stripe smuts on grasses are a highly polyphyletic group within Ustilaginomycotina, occurring in three genera, Tilletia, Urocystis, and Ustilago. Currently more than 12 Ustilago species inciting stripe smuts are recognised. The majority belong to the Ustilago striiformis-complex, with about 30 different taxa described from 165 different plant species. This study aims to assess whether host distinct-lineages can be observed amongst the Ustilago leaf-stripe smuts using nine different loci on a representative set. Phylogenetic reconstructions supported the monophyly of the Ustilago striiformis-complex that causes leaf-stripe and the polyphyly of other leaf-stripe smuts within Ustilago. Furthermore, smut specimens from the same host genus generally clustered together in well-supported clades that often had available species names for these lineages. In addition to already-named lineages, three new lineages were observed, and described as new species on the basis of host specificity and molecular differences: namely Ustilago jagei sp. nov. on Agrostis stolonifera, U. kummeri sp. nov. on Bromus inermis, and U. neocopinata sp. nov. on Dactylis glomerata.
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Affiliation(s)
- Julia Kruse
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | | | - Horst Zimmermann
- Cluster for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | | | - Udo Richter
- Traubenweg 8, 06632 Freyburg / Unstrut, Germany
| | | | - Marco Thines
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Cluster for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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Choi YJ, Beakes G, Glockling S, Kruse J, Nam B, Nigrelli L, Ploch S, Shin HD, Shivas RG, Telle S, Voglmayr H, Thines M. Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci. Mol Ecol Resour 2015; 15:1275-88. [PMID: 25728598 PMCID: PMC5736100 DOI: 10.1111/1755-0998.12398] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 11/30/2022]
Abstract
Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.
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Affiliation(s)
- Young-Joon Choi
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Gordon Beakes
- Division of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Julia Kruse
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Bora Nam
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Lisa Nigrelli
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Population Genetics,University of Duesseldorf, Universtitätsstr. 1, D-40225 Duesseldorf, Germany
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, Korea University, 136-701 Seoul, South Korea
| | - Roger G. Shivas
- Plant Pathology Herbarium, Biosecurity Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, 4001 Queensland, Australia
| | - Sabine Telle
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Hermann Voglmayr
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria
- Department of Forest and Soil Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Peter Jordan-Straße 82, 1190 Wien, Austria
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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Riess K, Bauer R, Kellner R, Kemler M, Piątek M, Vánky K, Begerow D. Identification of a new order of root-colonising fungi in the Entorrhizomycota: Talbotiomycetales ord. nov. on eudicotyledons. IMA Fungus 2015. [PMID: 26203418 PMCID: PMC4500077 DOI: 10.5598/imafungus.2015.06.01.07] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
The recently described fungal phylum Entorrhizomycota was established solely for the genus Entorrhiza, species of which cause root-galls in Cyperaceae and Juncaceae. Talbotiomyces calosporus (incertae sedis) shares morphological characteristics and an ecological niche with species of Entorrhiza. We investigated the higher classification of T. calosporus to determine whether it belongs in Entorrhizomycota. Ribosomal DNA sequences showed Talbotiomyces to be a close relative of Entorrhiza and both taxa form a highly supported monophyletic group. Based on molecular phylogenetic analyses and in congruence with existing morphological and ecological data, Entorrhiza and Talbotiomyces represent a deep dichotomy within the Entorrhizomycota. While species of Entorrhiza are characterised by dolipores and occur on monocotyledons, members of Talbotiomyces are characterised by simple pores and are associated with eudicotyledons. This expands the host range of the recently described Entorrhizomycota from Poales to other angiosperms. Higher taxa, namely Talbotiomycetales ord. nov. and Talbotiomycetaceae fam. nov., are proposed here to accommodate Talbotiomyces.
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Affiliation(s)
- Kai Riess
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076 Tübingen, Germany
| | - Robert Bauer
- University of Tübingen, Institute of Evolution and Ecology, Plant Evolutionary Ecology, Auf der Morgenstelle 1, 72076 Tübingen, Germany
| | - Ronny Kellner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Kemler
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Cnr Lynnwood and University Road, Hatfield 0083, Pretoria, South Africa
| | - Marcin Piątek
- W. Szafer Institute of Botany of the Polish Academy of Sciences, Department of Mycology, Lubicz 46, PL-31-512 Kraków, Poland
| | | | - Dominik Begerow
- University of Bochum, AG Geobotanik, Universitätsstraße 150, 44780 Bochum, Germany
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Choi YJ, Klosterman SJ, Kummer V, Voglmayr H, Shin HD, Thines M. Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach. Mol Phylogenet Evol 2015; 86:24-34. [PMID: 25772799 PMCID: PMC5736102 DOI: 10.1016/j.ympev.2015.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants.
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Affiliation(s)
- Young-Joon Choi
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.
| | | | - Volker Kummer
- University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 1, D-14469 Potsdam, Germany
| | - Hermann Voglmayr
- BOKU-University of Natural Resources and Life Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, Peter Jordan-Straße 82, 1190 Vienna, Austria; University of Vienna, Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, Rennweg 14, 1030 Wien, Austria
| | - Hyeon-Dong Shin
- Korea University, Division of Environmental Science and Ecological Engineering, Seoul 136-701, Republic of Korea
| | - Marco Thines
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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10
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Sharma R, Mishra B, Runge F, Thines M. Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. Genome Biol Evol 2014; 6:2034-49. [PMID: 25062916 PMCID: PMC4159001 DOI: 10.1093/gbe/evu148] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of Melanopsichium pennsylvanicum, closely related to Ustilago maydis and other Poaceae-infecting smuts, but parasitic to a dicot plant. To explore the evolutionary patterns resulting from host adaptation after this huge host jump, the genome of Me. pennsylvanicum was sequenced and compared with the genomes of U. maydis, Sporisorium reilianum, and U. hordei. Although all four genomes had a similar completeness in CEGMA (Core Eukaryotic Genes Mapping Approach) analysis, gene absence was highest in Me. pennsylvanicum, and most pronounced in putative secreted proteins, which are often considered as effector candidates. In contrast, the amount of private genes was similar among the species, highlighting that gene loss rather than gene gain is the hallmark of adaptation after the host jump to the dicot host. Our analyses revealed a trend of putative effectors to be next to another putative effector, but the majority of these are not in clusters and thus the focus on pathogenicity clusters might not be appropriate for all smut genomes. Positive selection studies revealed that Me. pennsylvanicum has the highest number and proportion of genes under positive selection. In general, putative effectors showed a higher proportion of positively selected genes than noneffector candidates. The 248 putative secreted effectors found in all four smut genomes might constitute a core set needed for pathogenicity, whereas those 92 that are found in all grass-parasitic smuts but have no ortholog in Me. pennsylvanicum might constitute a set of effectors important for successful colonization of grass hosts.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyCluster for Integrative Fungal Research (IPF), Frankfurt am Main, Germany
| | - Bagdevi Mishra
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, Stuttgart, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, GermanyInstitute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, GermanySenckenberg Gesellschaft für Naturforschung, Frankfurt am Main, GermanyCluster for Integrative Fungal Research (IPF), Frankfurt am Main, Germany
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11
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Christensen S, Heimes C, Agerbirk N, Kuzina V, Olsen CE, Hauser TP. Different Geographical Distributions of Two Chemotypes of Barbarea vulgaris that Differ in Resistance to Insects and a Pathogen. J Chem Ecol 2014; 40:491-501. [DOI: 10.1007/s10886-014-0430-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/16/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022]
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12
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Nigrelli L, Thines M. Tropical oomycetes in the German Bight – Climate warming or overlooked diversity? FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Homothallic sexual reproduction of Pustula helianthicola and germination of oospores. Fungal Biol 2012; 116:976-84. [DOI: 10.1016/j.funbio.2012.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 05/25/2012] [Accepted: 06/28/2012] [Indexed: 11/17/2022]
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14
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A new species of Pustula (Oomycetes, Albuginales) is the causal agent of sunflower white rust. Mycol Prog 2011. [DOI: 10.1007/s11557-011-0748-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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