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Backbones Trees for Important Phytopathogenic Genera: I (2014)

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Backbones Trees for Important Phytopathogenic Genera: I (2014) Fungal Diversity (2014) 67:21–125 DOI 10.1007/s13225-014-0298-1 One stop shop: backbones trees for important phytopathogenic genera: I (2014) Kevin D. Hyde & R. Henrik Nilsson & S. Aisyah Alias & Hiran A. Ariyawansa & Jaime E. Blair & Lei Cai & Arthur W. A. M. de Cock & Asha J. Dissanayake & Sally L. Glockling & Ishani D. Goonasekara & Michał Gorczak & Matthias Hahn & Ruvishika S. Jayawardena & Jan A. L. van Kan & Matthew H. Laurence & C. André Lévesque & Xinghong Li & Jian-Kui Liu & Sajeewa S. N. Maharachchikumbura & Dimuthu S. Manamgoda & Frank N. Martin & Eric H. C. McKenzie & Alistair R. McTaggart & Peter E. Mortimer & Prakash V. R. Nair & Julia Pawłowska & Tara L. Rintoul & Roger G. Shivas & Christoffel F. J. Spies & Brett A. Summerell & Paul W. J. Taylor & Razak B. Terhem & Dhanushka Udayanga & Niloofar Vaghefi & Grit Walther & Mateusz Wilk & Marta Wrzosek & Jian-Chu Xu & JiYe Yan & Nan Zhou Received: 6 June 2014 /Accepted: 16 July 2014 /Published online: 17 September 2014 # The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Many fungi are pathogenic on plants and cause and future research, this study provides phylogenetic syn- significant damage in agriculture and forestry. They are opses for 25 groups of plant pathogenic fungi in the also part of the natural ecosystem and may play a role in Ascomycota, Basidiomycota, Mucormycotina (Fungi), regulating plant numbers/density. Morphological identifi- and Oomycota, using recent molecular data, up-to-date cation and analysis of plant pathogenic fungi, while im- names, and the latest taxonomic insights. Lineage- portant, is often hampered by the scarcity of discrimina- specific laboratory protocols together with advice on their tory taxonomic characters and the endophytic or incon- application, as well as general observations, are also pro- spicuous nature of these fungi. Molecular (DNA se- vided. We hope to maintain updated backbone trees of quence) data for plant pathogenic fungi have emerged as these fungal lineages over time and to publish them joint- key information for diagnostic and classification studies, ly as new data emerge. Researchers of plant pathogenic although hampered in part by non-standard laboratory fungi not covered by the present study are invited to join practices and analytical methods. To facilitate current this future effort. Bipolaris, Botryosphaeriaceae, K. D. Hyde (*) : P. E. Mortimer : J.<C. Xu R. H. Nilsson Key Laboratory for Plant Diversity and Biogeography of East Asia, Department of Biological and Environmental Sciences, University of Kunming Institute of Botany, Chinese Academy of Sciences, Gothenburg, Box 461, 405 30 Göteborg, Sweden Kunming 650201, People’s Republic of China e-mail: [email protected] K. D. Hyde : S. A. Alias : S. S. N. Maharachchikumbura K. D. Hyde : P. E. Mortimer : J.<C. Xu Institute of Ocean and Earth Sciences (IOES), C308, Institute of World Agroforestry Centre, East Asia Node, Heilongtan, Postgraduate Studies Building, University of Malaya, Kunming 650201, People’s Republic of China 50603 Kuala Lumpur, Malaysia : : : K. D. Hyde H. A. Ariyawansa A. J. Dissanayake J. E. Blair : : < : I. D. Goonasekara R. S. Jayawardena: J. K. Liu : Department of Biology, Franklin & Marshall College, S. S. N. Maharachchikumbura D. S. Manamgoda D. Udayanga Lancaster, PA, USA Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand L. Cai : N. Zhou K. D. Hyde State Key Laboratory of Mycology, Institute of Microbiology, Botany and Microbiology Department, College of Science, King Chinese Academy of Sciences, Beijing 100101 Saud University, Riyadh 1145, Saudi Arabia People’sRepublicofChina 22 Fungal Diversity (2014) 67:21–125 Botryosphaeria, Botrytis, Choanephora, Colletotrichum, 8. Diaporthe–AJ Dissanayake, D Udayanga, JY Yan, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, XH Li, KD Hyde Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, 9. Diplodia AJ Dissanayake, JK Liu, JY Yan, XH Li, KD Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Hyde Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, 10. Dothiorella JK Liu, KD Hyde Ustilago and Verticillium are dealt with in this paper. 11. Fusarium–BSummerell,MH Laurence 12. Gilbertella–JPawłowska, G Walther, M Wilk, M Gorczak, M Wrzosek Keywords Ascomycota . Basidiomycota . Endophytes . 13. Lasiodiplodia JK Liu, KD Hyde Mucormycotina . Molecular identification . Oomycota . Plant 14. Mucor–JPawłowska, G Walther, M Wilk, M Gorczak, M pathogens . Protozoa Wrzosek 15. Neofusicoccum AJ Dissanayake, JK Liu, JY Yan, XH Li, KD Hyde Contents and contributors (main contributors underlined) 16. Pestalotiopsis–SSN Maharachchikumbura SA Alias KD Hyde 1. Bipolaris–DS Manamgoda, KD Hyde 17. Phyllosticta–NZhou,LCai 2. Botryosphaeriaceae–AJ Dissanayake, JK Liu, JY Yan, XH 18. Phytophthora–F Martin, JE Blair Li, KD Hyde 19. Puccinia–AR McTaggart, RG Shivas 3. Botryosphaeria–AJ Dissanayake, JK Liu, JY Yan, XH 20. Pyrenophora–HA Ariyawansa, KD Hyde Li, KD Hyde 21. Pythium–CFJ Spies, TL Rintoul, AWAM de Cock, SL 4. Botrytis–RB Terhem, MHahn,JAL van Kan Glockling, CA Lévesque 5. Choanephora–JPawłowska, G Walther, M Wilk, M 22. Rhizopus–M Gorczak, G Walther, J Pawłowska, M Gorczak, M Wrzosek Wilk, M Wrzosek 6. Colletotrichum–RS Jayawardena, DS Manamgoda, L Cai, 23. Stagonosporopsis–N Vaghefi, PWJ Taylor XHLi,JYYan,KDHyde 24. Ustilago–AR McTaggart, RG Shivas 7. Curvularia–DS Manamgoda, KD Hyde 25. Verticillium–PWJ Taylor, PVR Nair A. W. A. M. de Cock F. N. Martin CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, United States Department of Agriculture, Agriculture Research 3584CT Utrecht, The Netherlands Service, Salinas, CA, USA A. J. Dissanayake : R. S. Jayawardena : X. Li : J. Yan E. H. C. McKenzie Beijing Academy of Agriculture and Forestry Sciences, Institute of Landcare Research, Private Bag, 92170 Auckland, New Zealand Plant and Environment Protection, No. 9 of Shuguanghuayuanzhonglu, Haidian District, Beijing 100097, P. V. R. Nair : P. W. J. Taylor : N. Vaghefi People’sRepublicofChina Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia S. L. Glockling 135 Brodrick Road, Eastbourne BN22 9RA, East Sussex, UK A. R. McTaggart : R. G. Shivas Department of Agriculture, Fisheries and Forestry, Ecosciences M. Gorczak : J. Pawłowska : M. Wrzosek Precinct, Dutton Park, Queensland 4102, Australia Department of Plant Systematics and Geography, Faculty of Biology, University of Warsaw, Al. Ujazdowskie 4, 00-478, Warsaw, Poland R. B. Terhem Department of Forest Management, Faculty of Forestry, Universiti M. Hahn Putra Malaysia, 43400 Serdang, Malaysia Department of Biology, TU Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany G. Walther Leibniz-Institute for Natural Product Research and Infection J. A. L. van Kan : R. B. Terhem Biology–Hans-Knöll-Institute, Jena Microbial Resource Collection, Laboratory of Phytopathology, Wageningen University, Jena, Germany Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands G. Walther C. A. Lévesque : T. L. Rintoul : C. F. J. Spies Institute of Microbiology, Department of Microbiology and Agriculture and Agri-Food Canada, Central Experimental Farm, Molecular Biology, University of Jena, Jena, Germany Ottawa, ON, Canada M. Wilk M. H. Laurence : B. A. Summerell Inter-Faculty Interdisciplinary Doctoral Studies in Natural Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sciences and Mathematics, University of Warsaw, Warsaw, Sydney, New South Wales 2000, Australia Poland Fungal Diversity (2014) 67:21–125 23 Introduction pathogenic fungi require specialized extraction and PCR primers/protocols in order to amplify their DNA. Fungi form a large and heterogeneous eukaryotic kingdom Furthermore, the same genetic markers that give unparalleled with an estimated 1.5 million extant species. While all fungi phylogenetic resolution in some fungi may give none what- are heterotrophic, a wide range of nutritional strategies is soever in others. Many plant pathology studies focus on single known in the kingdom. Most of the ca. 100,000 described species of fungi, and recent revisions or synopses at the species of fungi are associated with plants through interactions generic or higher levels are lacking for the majority of plant including symbiosis, endophytism, saprotrophy and parasit- pathogenic fungi. ism (Stajich et al. 2009; Delaye et al. 2013; Persoh 2013; The present study seeks to facilitate present and future Hyde et al. 2013b). As plant parasites, fungi can cause signif- studies of plant pathogenic fungi by providing phylogenetic icant economic loss with far-reaching social implications and backbone trees for as many groups of fungi as our expertise consequences in agriculture, forestry and natural ecosystems allowed. Our ambition is to synthesize all recent molecular (Fisher et al. 2012). They are also part of the natural ecosystem data, recommendations on correct names, type material, geo/ and play an important role in regulation of species (Hantsch ecological observations, literature, and lineage-specific labo- et al. 2014). ratory advice into a comprehensive, uniform molecular trea- The study of plant pathogenic fungi–their systematics, tise for some of the largest and most widely encountered biology, and biological control–has a long and rich history lineages of plant pathogenic fungi. (Udayanga et al. 2011; Maharachchikumbura et al. 2011; Manamgoda et al. 2011). The inconspicuous
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