Publications by authors named "Marco Thines"

81 Publications

Setting scientific names at all taxonomic ranks in italics facilitates their quick recognition in scientific papers.

IMA Fungus 2020 Nov 17;11(1):25. Epub 2020 Nov 17.

Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.

It is common practice in scientific journals to print genus and species names in italics. This is not only historical as species names were traditionally derived from Greek or Latin. Importantly, it also facilitates the rapid recognition of genus and species names when skimming through manuscripts. However, names above the genus level are not always italicized, except in some journals which have adopted this practice for all scientific names. Since scientific names treated under the various Codes of nomenclature are without exception treated as Latin, there is no reason why names above genus level should be handled differently, particularly as higher taxon names are becoming increasingly relevant in systematic and evolutionary studies and their italicization would aid the unambiguous recognition of formal scientific names distinguishing them from colloquial names. Several leading mycological and botanical journals have already adopted italics for names of all taxa regardless of rank over recent decades, as is the practice in the International Code of Nomenclature for algae, fungi, and plants, and we hereby recommend that this practice be taken up broadly in scientific journals and textbooks.
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http://dx.doi.org/10.1186/s43008-020-00048-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7670697PMC
November 2020

sp. nov. (Oomycota, Peronosporales), a Downy Mildew Species Specialized to (Balsaminaceae).

Mycobiology 2020 Jul 13;48(4):304-312. Epub 2020 Jul 13.

Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.

Over the past 15 years, downy mildew became the most destructive foliar disease in cultivated species (Balsaminaceae) worldwide. A previous study had revealed that the causal agent was not (Oomycota, Peronosporales) but on , and on . This hints to a relatively high degree of specialization of on Balsaminaceae. Therefore, it was the aim of the present study to perform multigene phylogenetic analysis and detailed morphological investigation for several Korean downy mildew samples parasitic to cultivated , and , but also to a northeast Asian wild plant, . It was revealed that harbors a new species, which is introduced and described here as .
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http://dx.doi.org/10.1080/12298093.2020.1788259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476525PMC
July 2020

The Genome of (Brassicaceae) Provides Insights Into the Adaptation to Highly Calcareous Soils.

Front Plant Sci 2020 3;11:943. Epub 2020 Jul 3.

Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.

is widely distributed in temperate Eurasia, but restricted to Ca-rich habitats, predominantly on white Jurassic limestone, which is made up by calcium carbonate, with little other minerals. Thus, naturally occurring individuals are confronted with a high concentration of Ca ions while Mg ion concentration is relatively low. As there is a competitive uptake between these two ions, adaptation to the soil condition can be expected. In this study, it was the aim to explore the genomic consequences of this adaptation by sequencing and analysing the genome of . Its genome size is comparable with other diploid Brassicaceae, while more genes were predicted. Two Mg transporters known to be expressed in roots were duplicated and one showed a significant degree of positive selection. It is speculated that this evolved due to the pressure to take up Mg ions efficiently in the presence of an overwhelming amount of Ca ions. Future studies on plants specialized on similar soils and affinity tests of the transporters are needed to provide unequivocal evidence for this hypothesis. If verified, the transporters found in this study might be useful for breeding Brassicaceae crops for higher yield on Ca-rich and Mg -poor soils.
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http://dx.doi.org/10.3389/fpls.2020.00943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7350527PMC
July 2020

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus 2020 10;11:14. Epub 2020 Jul 10.

International Commission on the Taxonomy of Fungi, Champaign, IL USA.

True fungi () and fungus-like organisms (e.g. , ) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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http://dx.doi.org/10.1186/s43008-020-00033-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7353689PMC
July 2020

A glimpse into the biogeography, seasonality, and ecological functions of arctic marine .

IMA Fungus 2019 20;10. Epub 2019 Jun 20.

UiT-Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019 Tromsø, Norway.

High-latitude environments are warming, leading to changes in biological diversity patterns of taxa. are a group of fungal-like organisms that comprise a major clade of eukaryotic life and are parasites of fish, agricultural crops, and algae. The diversity, functionality, and distribution of these organisms are essentially unknown in the Arctic marine environment. Thus, it was our aim to conduct a first screening, using a functional gene assay and high-throughput sequencing of two gene regions within the 18S rRNA locus to examine the diversity, richness, and phylogeny of marine within Arctic sediment, seawater, and sea ice. We detected at every site sampled and identified regionally localized taxa, as well as taxa that existed in both Alaska and Svalbard. While the recently described diatom parasite made up about 50% of the oomycete reads found, many lineages were observed that could not be assigned to known species, including several that clustered with another recently described diatom parasite, . Across the Arctic, comprised a maximum of 6% of the entire eukaryotic microbial community in Barrow, Alaska May sediment and 10% in sea ice near the Svalbard archipelago. We found Arctic marine encode numerous genes involved in parasitism and carbon cycling processes. Ultimately, these data suggest that Arctic marine are a reservoir of uncharacterized biodiversity, the majority of which are probably parasites of diatoms, while others might cryptically cycle carbon or interface other unknown ecological processes. As the Arctic continues to warm, lower-latitude might migrate into the Arctic Ocean and parasitize non-coevolved hosts, leading to incalculable shifts in the primary producer community.
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http://dx.doi.org/10.1186/s43008-019-0006-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325649PMC
June 2019

The Genome of Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters.

Mol Plant Microbe Interact 2020 May 1;33(5):742-753. Epub 2020 Apr 1.

Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.

Along with , has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N scaffold length of around 248 kbp and an L scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of . has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
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http://dx.doi.org/10.1094/MPMI-07-19-0211-RDOI Listing
May 2020

Author Correction: The oomycete Lagenisma coscinodisci hijacks host alkaloid synthesis during infection of a marine diatom.

Nat Commun 2020 Mar 31;11(1):1698. Epub 2020 Mar 31.

Research Group Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41467-020-15527-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109102PMC
March 2020

Multiple evolutionary origins of sequestrate species in the agaricoid genus .

Mycologia 2020 Mar-Apr;112(2):400-422. Epub 2020 Mar 9.

Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany.

accommodates lamellate agaricoid species as well as sequestrate angiocarpic taxa, which do not form a monophyletic lineage within the genus. To clarify phylogenetic affinities and delimit species boundaries among sequestrate representatives of the genus, we analyzed historical and contemporary material from a broad geographic range, encompassing North America, southern Africa, eastern Asia, the Greek and Iberian peninsulas, and the Mediterranean islands of Cyprus and Lesvos. Six sequestrate lineages of were identified, which appear to have evolved in at least three independent gasteromycetation events. Multigene analysis of the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of the nuc 28S rDNA (28S), RNA polymerase II second largest subunit (), and translation elongation factor 1-α () genes revealed the presence of a previously undescribed species, introduced here as , sp. nov. Its sister species , previously known only from Spain, is shown to have a wider distribution throughout the Mediterranean basin. A South African collection of , a poorly known taxon described in 1840 and seldom appearing in literature since, was also shown to nest within . An epitype for this rare species is designated, becomes a priority synonym of , and nomenclatural implications are discussed. The phylogenetic placement of is confirmed after successful sequencing of the century-old holotype and an undescribed sister lineage of this species detected. Emended descriptions of sections , and are provided to reflect current results, along with updated descriptions and extensive imagery for all known sequestrate taxa of .
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http://dx.doi.org/10.1080/00275514.2020.1712179DOI Listing
March 2020

Promoter Activation in Δhfq Mutants as an Efficient Tool for Specialized Metabolite Production Enabling Direct Bioactivity Testing.

Angew Chem Int Ed Engl 2019 12 12;58(52):18957-18963. Epub 2019 Dec 12.

Mol. Biotechnol., Univ. Frankfurt, 60438, Frankfurt, Germany.

Natural products (NPs) from microorganisms have been important sources for discovering new therapeutic and chemical entities. While their corresponding biosynthetic gene clusters (BGCs) can be easily identified by gene-sequence-similarity-based bioinformatics strategies, the actual access to these NPs for structure elucidation and bioactivity testing remains difficult. Deletion of the gene encoding the RNA chaperone, Hfq, results in strains losing the production of most NPs. By exchanging the native promoter of a desired BGC against an inducible promoter in Δhfq mutants, almost exclusive production of the corresponding NP from the targeted BGC in Photorhabdus, Xenorhabdus and Pseudomonas was observed including the production of several new NPs derived from previously uncharacterized non-ribosomal peptide synthetases (NRPS). This easyPACId approach (easy Promoter Activated Compound Identification) facilitates NP identification due to low interference from other NPs. Moreover, it allows direct bioactivity testing of supernatants containing secreted NPs, without laborious purification.
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http://dx.doi.org/10.1002/anie.201910563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972681PMC
December 2019

The oomycete Lagenisma coscinodisci hijacks host alkaloid synthesis during infection of a marine diatom.

Nat Commun 2019 10 30;10(1):4938. Epub 2019 Oct 30.

Research Group Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany.

Flagellated oomycetes frequently infect unicellular algae, thus limiting their proliferation. Here we show that the marine oomycete Lagenisma coscinodisci rewires the metabolome of the bloom-forming diatom Coscinodiscus granii, thereby promoting infection success. The algal alkaloids β-carboline and 4-carboxy-2,3,4,9-tetrahydro-1H-β-carboline are induced during infection. Single-cell profiling with AP-MALDI-MS and confocal laser scanning microscopy reveals that algal carbolines accumulate in the reproductive form of the parasite. The compounds arrest the algal cell division, increase the infection rate and induce plasmolysis in the host. Our results indicate that the oomycete manipulates the host metabolome to support its own multiplication.
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http://dx.doi.org/10.1038/s41467-019-12908-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821873PMC
October 2019

An evolutionary framework for host shifts - jumping ships for survival.

Authors:
Marco Thines

New Phytol 2019 10 9;224(2):605-617. Epub 2019 Sep 9.

Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, D-60486, Frankfurt am Main, Germany.

Host jumping is a process by which pathogens settle in new host groups. It is a cornerstone in the evolution of pathogens, as it leads to pathogen diversification. It is unsurprising that host jumping is observed in facultative pathogens, as they can reproduce even if they kill their hosts. However, host jumps were thought to be rare in obligate biotrophic pathogens, but molecular phylogenetics has revealed that the opposite is true. Here, I review some concepts and recent findings and present several hypotheses on the matter. In short, pathogens evolve and diversify via host jumps, followed by radiation, specialisation and speciation. Host jumps are facilitated by, for example, effector innovations, stress, compatible pathogens and physiological similarities. Host jumping, subsequent establishment, and speciation takes place rapidly - within centuries and millennia rather than over millions of years. If pathogens are unable to evolve into neutral or mutualistic interactions with their hosts, they will eventually be removed from the host population, despite balancing trade-offs. Thus, generally, plant pathogens only survive in the course of evolution if they jump hosts. This is also reflected by the diversity patterns observed in many genera of plant pathogens, where it leads to a mosaic pattern of host groups over time, in which the original host group becomes increasingly obscure.
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http://dx.doi.org/10.1111/nph.16092DOI Listing
October 2019

Neofunctionalization of the secreted Tin2 effector in the fungal pathogen Ustilago maydis.

Nat Microbiol 2019 02 3;4(2):251-257. Epub 2018 Dec 3.

Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Plant-pathogenic fungi hijack their hosts by secreting effector proteins. Effectors serve to suppress plant immune responses and modulate the host metabolism to benefit the pathogen. Smut fungi are biotrophic pathogens that also parasitize important cereals, including maize. Symptom development is usually restricted to the plant inflorescences. Ustilago maydis is an exception in its ability to cause tumours in both inflorescences and leaves of maize, and in inducing anthocyanin biosynthesis through the secreted Tin2 effector. How the unique lifestyle of U. maydis has evolved remains to be elucidated. Here we show that Tin2 in U. maydis has been neofunctionalized. We functionally compared Tin2 effectors of U. maydis and the related smut Sporisorium reilianum, which results in symptoms only in the inflorescences of maize and fails to induce anthocyanin. We show that Tin2 effectors from both fungi target distinct paralogues of a maize protein kinase, leading to stabilization and inhibition, respectively. An ancestral Tin2 effector functionally replaced the virulence function of S. reilianum Tin2 but failed to induce anthocyanin, and was unable to substitute for Tin2 in U. maydis. This shows that Tin2 in U. maydis has acquired a specialized function, probably connected to the distinct pathogenic lifestyle of this fungus.
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http://dx.doi.org/10.1038/s41564-018-0304-6DOI Listing
February 2019

The first smut fungus, sp. nov. (Glomosporiaceae), described from (Asteraceae).

MycoKeys 2018 11(41):39-50. Epub 2018 Oct 11.

Goethe University Frankfurt am Main, Department of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.

There are 63 known species of (Glomosporiaceae, Ustilaginomycotina), a third of which occur on Asteraceae. These smut fungi produce yellowish-brown to reddish-brown masses of spore balls in specific, mostly regenerative, plant organs. A species of was collected in the flower heads of (Anthemideae, Asteraceae) on Rhodes Island, Greece, in 2015 and 2017, which represents the first smut record of a smut fungus on a host plant species in this tribe. Based on its distinctive morphology, host species and genetic divergence, this species is described as Molecular barcodes of the ITS region are provided for this and several other species of . A phylogenetic and morphological comparison to closely related species showed that differed from other species of . produced loose spore balls in the flower heads and peduncles of unlike other flower-infecting species.
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http://dx.doi.org/10.3897/mycokeys.41.28454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194141PMC
October 2018

Oomycetes.

Authors:
Marco Thines

Curr Biol 2018 08;28(15):R812-R813

Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany. Electronic address:

If it looks and acts like a fungus, it still might be-an Oomycete! Marco Thines introduces us to these fascinating fungal look-alikes.
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http://dx.doi.org/10.1016/j.cub.2018.05.062DOI Listing
August 2018

Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon.

IMA Fungus 2018 Jun 28;9(1):177-183. Epub 2018 May 28.

Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.

The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048572PMC
June 2018

Considerations and consequences of allowing DNA sequence data as types of fungal taxa.

Authors:
Juan Carlos Zamora Måns Svensson Roland Kirschner Ibai Olariaga Svengunnar Ryman Luis Alberto Parra József Geml Anna Rosling Slavomír Adamčík Teuvo Ahti M Catherine Aime A Martyn Ainsworth László Albert Edgardo Albertó Alberto Altés García Dmitry Ageev Reinhard Agerer Begoña Aguirre-Hudson Joe Ammirati Harry Andersson Claudio Angelini Vladimír Antonín Takayuki Aoki André Aptroot Didier Argaud Blanca Imelda Arguello Sosa Arne Aronsen Ulf Arup Bita Asgari Boris Assyov Violeta Atienza Ditte Bandini João Luís Baptista-Ferreira Hans-Otto Baral Tim Baroni Robert Weingart Barreto Henry Beker Ann Bell Jean-Michel Bellanger Francesco Bellù Martin Bemmann Mika Bendiksby Egil Bendiksen Katriina Bendiksen Lajos Benedek Anna Bérešová-Guttová Franz Berger Reinhard Berndt Annarosa Bernicchia Alona Yu Biketova Enrico Bizio Curtis Bjork Teun Boekhout David Boertmann Tanja Böhning Florent Boittin Carlos G Boluda Menno W Boomsluiter Jan Borovička Tor Erik Brandrud Uwe Braun Irwin Brodo Tatiana Bulyonkova Harold H Burdsall Bart Buyck Ana Rosa Burgaz Vicent Calatayud Philippe Callac Emanuele Campo Massimo Candusso Brigitte Capoen Joaquim Carbó Matteo Carbone Rafael F Castañeda-Ruiz Michael A Castellano Jie Chen Philippe Clerc Giovanni Consiglio Gilles Corriol Régis Courtecuisse Ana Crespo Cathy Cripps Pedro W Crous Gladstone Alves da Silva Meiriele da Silva Marjo Dam Nico Dam Frank Dämmrich Kanad Das Linda Davies Eske De Crop Andre De Kesel Ruben De Lange Bárbara De Madrignac Bonzi Thomas Edison E Dela Cruz Lynn Delgat Vincent Demoulin Dennis E Desjardin Paul Diederich Bálint Dima Maria Martha Dios Pradeep Kumar Divakar Clovis Douanla-Meli Brian Douglas Elisandro Ricardo Drechsler-Santos Paul S Dyer Ursula Eberhardt Damien Ertz Fernando Esteve-Raventós Javier Angel Etayo Salazar Vera Evenson Guillaume Eyssartier Edit Farkas Alain Favre Anna G Fedosova Mario Filippa Péter Finy Adam Flakus Simón Fos Jacques Fournier André Fraiture Paolo Franchi Ana Esperanza Franco Molano Gernot Friebes Andreas Frisch Alan Fryday Giuliana Furci Ricardo Galán Márquez Matteo Garbelotto Joaquina María García-Martín Mónica A García Otálora Dania García Sánchez Alain Gardiennet Sigisfredo Garnica Isaac Garrido Benavent Genevieve Gates Alice da Cruz Lima Gerlach Masoomeh Ghobad-Nejhad Tatiana B Gibertoni Tine Grebenc Irmgard Greilhuber Bella Grishkan Johannes Z Groenewald Martin Grube Gérald Gruhn Cécile Gueidan Gro Gulden Luis Fp Gusmão Josef Hafellner Michel Hairaud Marek Halama Nils Hallenberg Roy E Halling Karen Hansen Christoffer Bugge Harder Jacob Heilmann-Clausen Stip Helleman Alain Henriot Margarita Hernandez-Restrepo Raphaël Herve Caroline Hobart Mascha Hoffmeister Klaus Høiland Jan Holec Håkon Holien Karen Hughes Vit Hubka Seppo Huhtinen Boris Ivančević Marian Jagers Walter Jaklitsch AnnaElise Jansen Ruvishika S Jayawardena Thomas Stjernegaard Jeppesen Mikael Jeppson Peter Johnston Per Magnus Jørgensen Ingvar Kärnefelt Liudmila B Kalinina Gintaras Kantvilas Mitko Karadelev Taiga Kasuya Ivona Kautmanová Richard W Kerrigan Martin Kirchmair Anna Kiyashko Dániel G Knapp Henning Knudsen Kerry Knudsen Tommy Knutsson Miroslav Kolařík Urmas Kõljalg Alica Košuthová Attila Koszka Heikki Kotiranta Vera Kotkova Ondřej Koukol Jiří Kout Gábor M Kovács Martin Kříž Åsa Kruys Viktor Kučera Linas Kudzma Francisco Kuhar Martin Kukwa T K Arun Kumar Vladimír Kunca Ivana Kušan Thomas W Kuyper Carlos Lado Thomas Læssøe Patrice Lainé Ewald Langer Ellen Larsson Karl-Henrik Larsson Gary Laursen Christian Lechat Serena Lee James C Lendemer Laura Levin Uwe Lindemann Håkan Lindström Xingzhong Liu Regulo Carlos Llarena Hernandez Esteve Llop Csaba Locsmándi Deborah Jean Lodge Michael Loizides László Lőkös Jennifer Luangsa-Ard Matthias Lüderitz Thorsten Lumbsch Matthias Lutz Dan Mahoney Ekaterina Malysheva Vera Malysheva Patinjareveettil Manimohan Yasmina Marin-Felix Guilhermina Marques Rubén Martínez-Gil Guy Marson Gerardo Mata P Brandon Matheny Geir Harald Mathiassen Neven Matočec Helmut Mayrhofer Mehdi Mehrabi Ireneia Melo Armin Mešić Andrew S Methven Otto Miettinen Ana M Millanes Romero Andrew N Miller James K Mitchell Roland Moberg Pierre-Arthur Moreau Gabriel Moreno Olga Morozova Asunción Morte Lucia Muggia Guillermo Muñoz González Leena Myllys István Nagy László G Nagy Maria Alice Neves Tuomo Niemelä Pier Luigi Nimis Nicolas Niveiro Machiel E Noordeloos Anders Nordin Sara Raouia Noumeur Yuri Novozhilov Jorinde Nuytinck Esteri Ohenoja Patricia Oliveira Fiuza Alan Orange Alexander Ordynets Beatriz Ortiz-Santana Leticia Pacheco Ferenc Pál-Fám Melissa Palacio Zdeněk Palice Viktor Papp Kadri Pärtel Julia Pawlowska Aurelia Paz Ursula Peintner Shaun Pennycook Olinto Liparini Pereira Pablo Pérez Daniëls Miquel À Pérez-De-Gregorio Capella Carlos Manuel Pérez Del Amo Sergio Pérez Gorjón Sergio Pérez-Ortega Israel Pérez-Vargas Brian A Perry Jens H Petersen Ronald H Petersen Donald H Pfister Chayanard Phukhamsakda Marcin Piątek Meike Piepenbring Raquel Pino-Bodas Juan Pablo 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IMA Fungus 2018 Jun 24;9(1):167-175. Epub 2018 May 24.

Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11 International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048565PMC
June 2018

Competing sexual and asexual generic names in and () and recommendations for use.

IMA Fungus 2018 Jun 26;9(1):75-89. Epub 2018 Apr 26.

Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97333, USA.

With the change to one scientific name for pleomorphic fungi, generic names typified by sexual and asexual morphs have been evaluated to recommend which name to use when two names represent the same genus and thus compete for use. In this paper, generic names in and are evaluated based on their type species to determine which names are synonyms. Twenty-one sets of sexually and asexually typified names in and eight sets in were determined to be congeneric and compete for use. Recommendations are made as to which generic name to use. In most cases the principle of priority is followed. However, eight generic names in the , and none in , are recommended for protection: over , over , over and over over over , over and , and over In addition, eight new combinations are made: , and combs. nov.
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http://dx.doi.org/10.5598/imafungus.2018.09.01.06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048570PMC
June 2018

species causing leaf-stripe smut revisited.

IMA Fungus 2018 Jun 20;9(1):49-73. Epub 2018 Mar 20.

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.

Leaf-stripe smuts on grasses are a highly polyphyletic group within , occurring in three genera, , , and . Currently more than 12 species inciting stripe smuts are recognised. The majority belong to the -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 leaf-stripe smuts using nine different loci on a representative set. Phylogenetic reconstructions supported the monophyly of the -complex that causes leaf-stripe and the polyphyly of other leaf-stripe smuts within . 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 sp. nov. on , sp. nov. on , and sp. nov. on
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http://dx.doi.org/10.5598/imafungus.2018.09.01.05DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048562PMC
June 2018

A reference genome of the European beech (Fagus sylvatica L.).

Gigascience 2018 06;7(6)

Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.

Background: The European beech is arguably the most important climax broad-leaved tree species in Central Europe, widely planted for its valuable wood. Here, we report the 542 Mb draft genome sequence of an up to 300-year-old individual (Bhaga) from an undisturbed stand in the Kellerwald-Edersee National Park in central Germany.

Findings: Using a hybrid assembly approach, Illumina reads with short- and long-insert libraries, coupled with long Pacific Biosciences reads, we obtained an assembled genome size of 542 Mb, in line with flow cytometric genome size estimation. The largest scaffold was of 1.15 Mb, the N50 length was 145 kb, and the L50 count was 983. The assembly contained 0.12% of Ns. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis retrieved 94% complete BUSCO genes, well in the range of other high-quality draft genomes of trees. A total of 62,012 protein-coding genes were predicted, assisted by transcriptome sequencing. In addition, we are reporting an efficient method for extracting high-molecular-weight DNA from dormant buds, by which contamination by environmental bacteria and fungi was kept at a minimum.

Conclusions: The assembled genome will be a valuable resource and reference for future population genomics studies on the evolution and past climate change adaptation of beech and will be helpful for identifying genes, e.g., involved in drought tolerance, in order to select and breed individuals to adapt forestry to climate change in Europe. A continuously updated genome browser and download page can be accessed from beechgenome.net, which will include future genome versions of the reference individual Bhaga, as new sequencing approaches develop.
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http://dx.doi.org/10.1093/gigascience/giy063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6014182PMC
June 2018

The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes.

BMC Genomics 2018 01 15;19(1):48. Epub 2018 Jan 15.

Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany.

Background: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology.

Results: Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation. In terms of fruit body development, our analyses revealed a conserved repertoire of fruiting-related genes, which corresponds well to the archetypal fruit body morphology of this mushroom. For some genes involved in fruit body formation, paralogisation was observed, but not all fruit body maturation-associated genes known from other agaricomycetes seem to be conserved in the genome sequence of A. aegerita. In terms of lytic enzymes, our analyses suggest a versatile arsenal of biopolymer-degrading enzymes that likely account for the flexible life style of this species. Regarding the amount of genes encoding CAZymes relevant for lignin degradation, A. aegerita shows more similarity to white-rot fungi than to litter decomposers, including 18 genes coding for unspecific peroxygenases and three dye-decolourising peroxidase genes expanding its lignocellulolytic machinery.

Conclusions: The genome resource will be useful for developing strategies towards genetic manipulation of A. aegerita, which will subsequently allow functional genetics approaches to elucidate fundamentals of fruiting and vegetative growth including lignocellulolysis.
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http://dx.doi.org/10.1186/s12864-017-4430-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769442PMC
January 2018

Facultative root-colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species.

New Phytol 2018 02 2;217(3):1190-1202. Epub 2017 Nov 2.

Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany.

There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors. The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples. HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences. Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.
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http://dx.doi.org/10.1111/nph.14873DOI Listing
February 2018

Asexual and sexual morphs of revisited.

IMA Fungus 2017 Jun 15;8(1):117-129. Epub 2017 May 15.

Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60486 Frankfurt am Main, Germany.

Yeasts of the now unused asexually typified genus belong to the smut fungi () and are mostly believed to be apathogenic asexual yeasts derived from smut fungi that have lost pathogenicity on plants. However, phylogenetic studies have shown that most species are phylogenetically close to smut fungi parasitic to plants, suggesting that some of the species might represent adventitious isolations of the yeast morph of otherwise plant pathogenic smut fungi. However, there are some species, such as (syn. ) that are isolated throughout the world and sometimes are also found in clinical samples and do not have a known plant pathogenic sexual morph. In this study, it is revealed by phylogenetic investigations that isolates of the biocontrol agent are interspersed with sexual lineages, suggesting conspecificity. This raises doubts regarding the apathogenic nature of asexual morphs previously placed in , but suggests that there might also be pathogenic sexual morph counterparts for those species known only from asexual morphs. The finding that several additional species currently only known from their yeast morphs are embedded within the genus , suggests that the yeast morph might play a more dominant role in this genus as compared to other genera of . In addition, phylogenetic reconstructions demonstrated that has a narrow host range and that some previously described but not widely used species names should be applied for on other host genera than .
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http://dx.doi.org/10.5598/imafungus.2017.08.01.09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493530PMC
June 2017

Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation.

Mol Ecol 2017 Sep 2;26(18):4618-4630. Epub 2017 Aug 2.

Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.

Studying community structure and dynamics of plant-associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS-based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta-tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter- and intraspecific biotic interactions, may be more important for the local assembly of their communities.
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http://dx.doi.org/10.1111/mec.14231DOI Listing
September 2017

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

PLoS One 2017 26;12(4):e0175808. Epub 2017 Apr 26.

University Koblenz-Landau, Institute of Environmental Science, Landau in der Pfalz, Germany.

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175808PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405915PMC
September 2017

Adaptive differentiation coincides with local bioclimatic conditions along an elevational cline in populations of a lichen-forming fungus.

BMC Evol Biol 2017 Mar 31;17(1):93. Epub 2017 Mar 31.

Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.

Background: Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments.

Results: We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction.

Conclusions: Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.
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http://dx.doi.org/10.1186/s12862-017-0929-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374679PMC
March 2017

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants.

ISME J 2017 03 1;11(3):777-790. Epub 2016 Nov 1.

Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany.

Plants associate through their roots with fungal assemblages that impact their abundance and productivity. Non-mycorrhizal endophytes constitute an important component of such fungal diversity, but their implication in ecosystem processes is little known. Using a selection of 128 root-endophytic strains, we defined functional groups based on their traits and plant interactions with potential to predict community assembly and symbiotic association processes. In vitro tests of the strains' interactions with Arabidopsis thaliana, Microthlaspi erraticum and Hordeum vulgare showed a net negative effect of fungal colonization on plant growth. The effects partly depended on the phylogenetic affiliation of strains, but also varied considerably depending on the plant-strain combination. The variation was partly explained by fungal traits shared by different lineages, like growth rates or melanization. The origin of strains also affected their symbioses, with endophytes isolated from Microthlaspi spp. populations being more detrimental to M. erraticum than strains from other sources. Our findings suggest that plant-endophyte associations are subject to local processes of selection, in which particular combinations of symbionts are favored across landscapes. We also show that different common endophytic taxa have differential sets of traits found to affect interactions, hinting to a functional complementarity that can explain their frequent co-existence in natural communities.
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http://dx.doi.org/10.1038/ismej.2016.140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322293PMC
March 2017

Genome comparisons provide insights into the role of secondary metabolites in the pathogenic phase of the Photorhabdus life cycle.

BMC Genomics 2016 08 3;17:537. Epub 2016 Aug 3.

Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe Universität Frankfurt, Frankfurt am Main, Germany.

Background: Bacteria within the genus Photorhabdus maintain mutualistic symbioses with nematodes in complicated lifecycles that also involves insect pathogenic phases. Intriguingly, these bacteria are rich in biosynthetic gene clusters that produce compounds with diverse biological activities. As a basis to better understand the life cycles of Photorhabdus we sequenced the genomes of two recently discovered representative species and performed detailed genomic comparisons with five publically available genomes.

Results: Here we report the genomic details of two new reference Photorhabdus species. By then conducting genomic comparisons across the genus, we show that there are several highly conserved biosynthetic gene clusters. These clusters produce a range of bioactive small molecules that support the pathogenic phase of the integral relationship that Photorhabdus maintain with nematodes.

Conclusions: Photorhabdus contain several genetic loci that allow them to become specialist insect pathogens by efficiently evading insect immune responses and killing the insect host.
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http://dx.doi.org/10.1186/s12864-016-2862-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971723PMC
August 2016

Detection and Quantification of Bremia lactucae by Spore Trapping and Quantitative PCR.

Phytopathology 2016 11 29;106(11):1426-1437. Epub 2016 Aug 29.

First and tenth authors: Department of Plant Pathology, University of California-Davis, 1636 E. Alisal St. Salinas 93901; second, third, and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), 1636 E. Alisal St., Salinas, CA 93905; fourth author: Kunsan National University, Department of Biology, Gunsan 54150, Republic of Korea; fourth and fifth authors: Biodiversity and Climate Research Center (BiK-F) Senckenberg Gesellscharft für Naturforschung, D-60325 Frankfurt am Main, and Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60325 Frankfurt am Main, Germany; sixth author: The Genome Center and Department of Plant Sciences, University of California, Davis 95616; seventh author: University of California Cooperative Extension, Monterey County, Salinas; eighth author: The Genome Center and Department of Plant Pathology, University of California, Davis; and ninth author: USDA-ARS, Corvallis, OR.

Bremia lactucae is an obligate, oomycete pathogen of lettuce that causes leaf chlorosis and necrosis and adversely affects marketability. The disease has been managed with a combination of host resistance and fungicide applications with success over the years. Fungicide applications are routinely made under the assumption that inoculum is always present during favorable environmental conditions. This approach often leads to fungicide resistance in B. lactucae populations. Detection and quantification of airborne B. lactucae near lettuce crops provides an estimation of the inoculum load, enabling more judicious timing of fungicide applications. We developed a quantitative polymerase chain reaction (qPCR)-based assay using a target sequence in mitochondrial DNA for specific detection of B. lactucae. Validation using amplicon sequencing of DNA from 83 geographically diverse isolates, representing 14 Bremia spp., confirmed that the primers developed for the TaqMan assays are species specific and only amplify templates from B. lactucae. DNA from a single sporangium could be detected at a quantification cycle (C) value of 32, and C values >35 were considered to be nonspecific. The coefficient of determination (R) for regression between sporangial density derived from flow cytometry and C values derived from the qPCR was 0.86. The assay was deployed using spore traps in the Salinas Valley, where nearly half of U.S. lettuce is produced. The deployment of this sensitive B. lactucae-specific assay resulted in the detection of the pathogen during the 2-week lettuce-free period as well as during the cropping season. These results demonstrate that this assay will be useful for quantifying inoculum load in and around the lettuce fields for the purpose of timing fungicide applications based on inoculum load.
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http://dx.doi.org/10.1094/PHYTO-03-16-0143-RDOI Listing
November 2016

Baobabopsis, a new genus of graminicolous downy mildews from tropical Australia, with an updated key to the genera of downy mildews.

IMA Fungus 2015 Dec 25;6(2):483-91. Epub 2015 Nov 25.

Plant Pathology Herbarium, Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, Qld 4001, Australia.

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.
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http://dx.doi.org/10.5598/imafungus.2015.06.02.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681264PMC
December 2015

Evolution, Diversity, and Taxonomy of the Peronosporaceae, with Focus on the Genus Peronospora.

Phytopathology 2016 Jan 9;106(1):6-18. Epub 2015 Dec 9.

First and second authors: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; and Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; and first author: Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; and second author: Kunsan National University, Department of Biology, Gunsan 54150, Korea.

Downy mildews are a notorious group of oomycete plant pathogens, causing high economic losses in various crops and ornamentals. The most species-rich genus of oomycetes is the genus Peronospora. This review provides a wide overview of these pathogens, ranging from macro- and micro-evolutionary patterns, their biodiversity and ecology to short overviews for the currently economically most important pathogens and potential emerging diseases. In this overview, the taxonomy of economically relevant species is also discussed, as the application of the correct names and species concepts is a prerequisite for effective quarantine regulations and phytosanitary measures.
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http://dx.doi.org/10.1094/PHYTO-05-15-0127-RVWDOI Listing
January 2016