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Aspergillus Systematics in the Genomic Era Studies in Mycology 59 (2007) Aspergillus systematics in the genomic era Robert A. Samson and János Varga CBS Fungal Biodiversity Centre, Utrecht, The Netherlands An institute of the Royal Netherlands Academy of Arts and Sciences Aspergillus systematics in the genomic era STUDIE S IN MYCOLOGY 59, 2007 Studies in Mycology The Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and in rare occasions the proceedings of special meetings related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. For instructions for authors see www.cbs.knaw.nl. EXECUTIVE EDITOR Prof. dr Robert A. Samson, CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. E-mail: [email protected] LAYOUT EDITOR Manon van den Hoeven-Verweij, CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. E-mail: [email protected] SCIENTIFIC EDITOR S Prof. dr Uwe Braun, Martin-Luther-Universität, Institut für Geobotanik und Botanischer Garten,Herbarium, Neuwerk 21, D-06099 Halle, Germany. E-mail: [email protected] Prof. dr Pedro W. Crous, CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. E-mail: [email protected] Prof. dr David M. Geiser, Department of Plant Pathology, 121 Buckhout Laboratory, Pennsylvania State University, University Park, PA, U.S.A. 16802. E-mail: [email protected] Dr Lorelei L. Norvell, Pacific Northwest Mycology Service, 6720 NW Skyline Blvd, Portland, OR, U.S.A. 97229-1309. E-mail: [email protected] Dr Erast Parmasto, Institute of Zoology & Botany, 181 Riia Street, Tartu, Estonia EE-51014. E-mail: [email protected] Prof. dr Alan J.L. Phillips, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta de Torre, 2829-516 Caparica, Portugal. E-mail: [email protected] Dr Amy Y. Rossman, Rm 304, Bldg 011A, Systematic Botany & Mycology Laboratory, Beltsville, MD, U.S.A. 20705. E-mail: [email protected] Dr Keith A. Seifert, Research Scientist / Biodiversity (Mycology and Botany), Agriculture & Agri-Food Canada, KW Neatby Bldg, 960 Carling Avenue, Ottawa, ON, Canada K1A OC6. E-mail: [email protected] Prof. dr Jeffrey K. Stone, Department of Botany & Plant Pathology, Cordley 2082, Oregon State University, Corvallis, OR, U.S.A. 97331-2902. E-mail: [email protected] Dr Richard C. Summerbell, 27 Hillcrest Park, Toronto, Ont. M4X 1E8, Canada. E-mail: [email protected] Copyright 2007 CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. You are free to share — to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by- nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author"s moral rights. Publication date: 15 December 2007 Published and distributed by CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. Internet: www.cbs.knaw.nl. E-mail: [email protected]. ISBN/EAN : 978-90-70351-69-4 Online ISSN : 1872-9797 Print ISSN : 0166-0616 Cover: Top from left to right. Conidiophores Aspergillus clavatus, A. fumigatus, A. longivesica. Bottom from left to right. Scanning electron micrograhs of Neosartorya denticulata, Petri dish with DG 18 agar and coffee beans from Thailand showing Aspergillus colonies, conidophores of A. terreus. Aspergillus systematics in the genomic era edited by Robert A. Samson CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands János Varga CBS Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; Department of Microbiology, Faculty of Sciences, University of Szeged, H-6701 Szeged, P.O. Box 533, Hungary CBS Fungal Biodiversity Centre, Utrecht, The Netherlands An institute of the Royal Netherlands Academy of Arts and Sciences CONTENTS D.M. Geiser, M.A. Klich, J.C. Frisvad, S.W. Peterson, J. Varga and R.A. Samson: The current status of species recognition and identification in Aspergillus ............................................................................................................................................................................................. 1 A. Rokas, G. Payne, N.D. Fedorova, S.E. Baker, M. Machida, J. Yu, D. R, Georgianna, R. A. Dean, D. Bhatnagar, T.E. Cleveland, J.R. Wortman, R. Maiti, V. Joardar, P. Amedeo, D.W. Denning and W.C. Nierman: What can comparative genomics tell us about species concepts in the genus Aspergillus? ............................................................................................................................................ 11 K. Pál, A.D. van Diepeningen, J. Varga, R.F. Hoekstra, P.S. Dyer and A.J.M. Debets: Sexual and vegetative compatibility genes in the aspergilli ................................................................................................................................................................................................... 19 J.C. Frisvad, T.O. Larsen, R. de Vries, M. Meijer, J. Houbraken, F.J. Cabañes, K. Ehrlich and R.A. Samson: Secondary metabolite profiling, growth profiles and other tools for species recognition and important Aspergillus mycotoxins ................................................................ 31 S.A. Balajee, J. Houbraken, P.E. Verweij, S-B. Hong, T. Yaguchi, J. Varga and R.A. Samson: Aspergillus species identification in the clinical setting ....................................................................................................................................................................................................... 39 C.H.W. Klaassen and N. Osherov: Aspergillus Strain Typing in the Genomics Era ....................................................................................... 47 G. Perrone, A. Susca, G. Cozzi, K.Ehrlich, J. Varga, J.C. Frisvad, M. Meijer, P. Noonim, Warapa Mahakarnchanakul and R.A. Samson: Biodiversity of Aspergillus species in some important agricultural products ............................................................................................ 53 J.I. Pitt and R.A. Samson: Nomenclatural considerations in naming species of Aspergillus and its teleomorphs ......................................... 67 R.A. Samson, J. Varga, S.M. Witiak and D.M. Geiser: The species concept in Aspergillus: recommendations of an international panel ..... 71 J. Varga, J.C. Frisvad and R.A. Samson: Polyphasic taxonomy of Aspergillus section Candidi based on molecular, morphological and physiological data ..................................................................................................................................................................................... 75 J. Varga, M. Due, J.C. Frisvad and R.A. Samson: Taxonomic revision of Aspergillus section Clavati based on molecular, morphological and physiological data ..................................................................................................................................................................................... 89 J. Houbraken, M. Due, J. Varga, M. Meijer, J.C. Frisvad and R.A. Samson: Polyphasic taxonomy of Aspergillus section Usti .................. 107 R.A. Samson, P. Noonim, M. Meijer, J. Houbraken, J.C. Frisvad and J. Varga: Diagnostic tools to identify black aspergilli ....................... 129 R.A. Samson, S. Hong, S.W. Peterson, J.C. Frisvad and J. Varga: Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya ............................................................................................................................................................................................ 147 PREFACE Since Pier Antonio Micheli described Aspergillus is his Nova Plantarum Genera in 1729 the genus attracted an immense interest. Many species were found as spoilage agents, or responsible for human and animal diseases. On the other hand aspergilli were also found as beneficial micro organisms in the fermentation of Asian food and beverages. With the discovery of aflatoxins, the interest and research of the aspergilli increased even more. In the present days Aspergillus research has grown to such a level, that it could be stated that aspergilli might be the most studied fungi. In all these applied fields, the basic systematics has always been very difficult and many mycologists have tried to propose a stable taxonomic classification based on their respective species concept. Although the taxonomy and subsequently the identification of most species has improved, the species concept of many species is still unclear. With the development of various molecular methods new approaches are proposed but it is clear that there is an urgent need to come to a standardisation and consensus how a species in Aspergillus is designated. Aspergillus is also in the forefront with respect to our genetic knowledge of fungi and with the complete genome sequences of nine Aspergillus species (Emericella nidulans, A. oryzae,
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