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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [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: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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de Oliveira TC, Freyria NJ, Sarmiento-Villamil JL, Porth I, Tanguay P, Bernier L. Unraveling the transcriptional features and gene expression networks of pathogenic and saprotrophic Ophiostoma species during the infection of Ulmus americana. Microbiol Spectr 2024; 12:e0369423. [PMID: 38230934 PMCID: PMC10845970 DOI: 10.1128/spectrum.03694-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
American elm (Ulmus americana), highly prized for its ornamental value, has suffered two successive outbreaks of Dutch elm disease (DED) caused by ascomycete fungi belonging to the genus Ophiostoma. To identify the genes linked to the pathogenicity of different species and lineages of Ophiostoma, we inoculated 2-year-old U. americana saplings with six strains representing three species of DED fungi, and one strain of the saprotroph Ophiostoma quercus. Differential expression analyses were performed following RNA sequencing of fungal transcripts recovered at 3- and 10-days post-infection. Based on a total of 8,640 Ophiostoma genes, we observed a difference in fungal gene expression depending on the strain inoculated and the time of incubation in host tissue. Some genes overexpressed in the more virulent strains of Ophiostoma encode hydrolases that possibly act synergistically. A mutant of Ophiostoma novo-ulmi in which the gene encoding the ogf1 transcription factor had been deleted did not produce transcripts for the gene encoding the hydrophobin cerato-ulmin and was less virulent. Weighted gene correlation network analyses identified several candidate pathogenicity genes distributed among 13 modules of interconnected genes.IMPORTANCEOphiostoma is a genus of cosmopolitan fungi that belongs to the family Ophiostomataceae and includes the pathogens responsible for two devastating pandemics of Dutch elm disease (DED). As the mechanisms of action of DED agents remain unclear, we carried out the first comparative transcriptomic study including representative strains of the three Ophiostoma species causing DED, along with the phylogenetically close saprotrophic species Ophiostoma quercus. Statistical analyses of the fungal transcriptomes recovered at 3 and 10 days following infection of Ulmus americana saplings highlighted several candidate genes associated with virulence and host-pathogen interactions wherein each strain showed a distinct transcriptome. The results of this research underscore the importance of investigating the transcriptional behavior of different fungal taxa to understand their pathogenicity and virulence in relation to the timeline of infection.
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Affiliation(s)
- Thais C. de Oliveira
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
| | - Nastasia J. Freyria
- Department of Natural Resource Sciences, McGill University, St. Anne-de-Bellevue, Quebec, Quebec, Canada
| | - Jorge Luis Sarmiento-Villamil
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
- Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IHSM-CSIC-UMA), Estación Experimental “La Mayora”, Málaga, Spain
| | - Ilga Porth
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Quebec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
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Cheng T, Veselská T, Křížková B, Švec K, Havlíček V, Stadler M, Kolařík M. Insight into the genomes of dominant yeast symbionts of European spruce bark beetle, Ips typographus. Front Microbiol 2023; 14:1108975. [PMID: 37077248 PMCID: PMC10106607 DOI: 10.3389/fmicb.2023.1108975] [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: 11/28/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Spruce bark beetle Ips typographus can trigger outbreaks on spruce that results in significant losses in the forest industry. It has been suggested that symbiotic microorganisms inhabiting the gut of bark beetles facilitate the colonization of plant tissues as they play a role in the detoxification of plant secondary metabolites, degrade plant cell wall and ameliorate beetle's nutrition. In this study, we sequenced and functionally annotated the genomes of five yeasts Kuraishia molischiana, Cryptococcus sp., Nakazawaea ambrosiae, Ogataea ramenticola, and Wickerhamomyces bisporus isolated from the gut of Ips typographus. Genome analysis identified 5314, 7050, 5722, 5502, and 5784 protein coding genes from K. molischiana, Cryptococcus sp., N. ambrosiae, O. ramenticola, and W. bisporus, respectively. Protein-coding sequences were classified into biological processes, cellular and molecular function based on gene ontology terms enrichment. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation was used to predict gene functions. All analyzed yeast genomes contain full pathways for the synthesis of essential amino acids and vitamin B6, which have nutritional importance to beetle. Furthermore, their genomes contain diverse gene families related to the detoxification processes. The prevalent superfamilies are aldo-keto reductase, ATP-binding cassette and the major facilitator transporters. The phylogenetic relationships of detoxification-related enzymes aldo-keto reductase, and cytochrome P450 monooxygenase, and ATP-binding cassette are presented. Genome annotations also revealed presence of genes active in lignocellulose degradation. In vitro analyses did not confirm enzymatic endolytic degradation of lignocellulose; however, all species can utilize and pectin and produce a large spectrum of exolytic enzymes attacking cellulose, chitin, and lipids.
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Affiliation(s)
- Tian Cheng
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tereza Veselská
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
| | - Barbora Křížková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
| | - Karel Švec
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
| | - Václav Havlíček
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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Fijarczyk A, Bernier L, Sakalidis ML, Medina-Mora CM, Porth I. Independent Evolution Has Led to Distinct Genomic Signatures in Dutch Elm Disease-Causing Fungi and Other Vascular Wilts-Causing Fungal Pathogens. J Fungi (Basel) 2022; 9:2. [PMID: 36675823 PMCID: PMC9864908 DOI: 10.3390/jof9010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Vascular wilts are important diseases caused by plant pathogenic fungi that result in the rapid death of their plant hosts. This is due to a systemic defense mechanism whereby the plant induces the compartmentalization of the infected vascular system in order to reduce the propagation of the fungus. The ascomycete class Sordariomycetes contains several species that cause vascular wilts in diverse plant hosts, and they can be classified into four taxonomic orders. The genetic mechanisms of pathogenesis have already been investigated in Fusarium and Verticillium species, but they have not yet been compared with other well-known wilt-causing species, especially fungi causing oak wilt or Dutch elm disease (DED). Here we analyzed 20 whole genome assemblies of wilt-causing fungi together with 56 other species using phylogenetic approaches to trace expansions and contractions of orthologous gene families and gene classes related to pathogenicity. We found that the wilt-causing pathogens evolved seven times, experiencing the largest fold changes in different classes of genes almost every time. However, some similarities exist across groups of wilt pathogens, particularly in Microascales and Ophiostomatales, and these include the common gains and losses of genes that make up secondary metabolite clusters (SMC). DED pathogens do not experience large-scale gene expansions, with most of the gene classes, except for some SMC families, reducing in number. We also found that gene family expansions in the most recent common ancestors of wilt pathogen groups are enriched for carbohydrate metabolic processes. Our study shows that wilt-causing species evolve primarily through distinct changes in their repertoires of pathogenicity-related genes and that there is the potential importance of carbohydrate metabolism genes for regulating osmosis in those pathogens that penetrate the plant vascular system.
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Affiliation(s)
- Anna Fijarczyk
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et Des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et Des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Département des Sciences du Bois et de la Forêt, Université Laval, Québec, QC G1V 0A6, Canada
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, QC G1V 0A6, Canada
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Carmen M Medina-Mora
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Ilga Porth
- Institut de Biologie Intégrative et Des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
- Département des Sciences du Bois et de la Forêt, Université Laval, Québec, QC G1V 0A6, Canada
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, QC G1V 0A6, Canada
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6
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Nigg M, de Oliveira TC, Sarmiento-Villamil JL, de la Bastide PY, Hintz WE, Sherif SM, Shukla M, Bernier L, Saxena PK. Comparative Analysis of Transcriptomes of Ophiostoma novo-ulmi ssp. americana Colonizing Resistant or Sensitive Genotypes of American Elm. J Fungi (Basel) 2022; 8:637. [PMID: 35736120 PMCID: PMC9224576 DOI: 10.3390/jof8060637] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/26/2022] [Accepted: 06/11/2022] [Indexed: 12/10/2022] Open
Abstract
The Ascomycete Ophiostoma novo-ulmi threatens elm populations worldwide. The molecular mechanisms underlying its pathogenicity and virulence are still largely uncharacterized. As part of a collaborative study of the O. novo-ulmi-elm interactome, we analyzed the O. novo-ulmi ssp. americana transcriptomes obtained by deep sequencing of messenger RNAs recovered from Ulmus americana saplings from one resistant (Valley Forge, VF) and one susceptible (S) elm genotypes at 0 and 96 h post-inoculation (hpi). Transcripts were identified for 6424 of the 8640 protein-coding genes annotated in the O. novo-ulmi nuclear genome. A total of 1439 genes expressed in planta had orthologs in the PHI-base curated database of genes involved in host-pathogen interactions, whereas 472 genes were considered differentially expressed (DEG) in S elms (370 genes) and VF elms (102 genes) at 96 hpi. Gene ontology (GO) terms for processes and activities associated with transport and transmembrane transport accounted for half (27/55) of GO terms that were significantly enriched in fungal genes upregulated in S elms, whereas the 22 GO terms enriched in genes overexpressed in VF elms included nine GO terms associated with metabolism, catabolism and transport of carbohydrates. Weighted gene co-expression network analysis identified three modules that were significantly associated with higher gene expression in S elms. The three modules accounted for 727 genes expressed in planta and included 103 DEGs upregulated in S elms. Knockdown- and knockout mutants were obtained for eight O. novo-ulmi genes. Although mutants remained virulent towards U. americana saplings, we identified a large repertoire of additional candidate O. novo-ulmi pathogenicity genes for functional validation by loss-of-function approaches.
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Affiliation(s)
- Martha Nigg
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (T.C.d.O.); (J.L.S.-V.)
| | - Thais C. de Oliveira
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (T.C.d.O.); (J.L.S.-V.)
| | - Jorge L. Sarmiento-Villamil
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (T.C.d.O.); (J.L.S.-V.)
| | - Paul Y. de la Bastide
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada; (P.Y.d.l.B.); (W.E.H.)
| | - Will E. Hintz
- Department of Biology, Centre for Forest Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada; (P.Y.d.l.B.); (W.E.H.)
| | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA;
| | - Mukund Shukla
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Louis Bernier
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (T.C.d.O.); (J.L.S.-V.)
| | - Praveen K. Saxena
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada;
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7
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Moravčík M, Mamoňová M, Račko V, Kováč J, Dvořák M, Krajňáková J, Ďurkovič J. Different Responses in Vascular Traits between Dutch Elm Hybrids with a Contrasting Tolerance to Dutch Elm Disease. J Fungi (Basel) 2022; 8:215. [PMID: 35330217 PMCID: PMC8954630 DOI: 10.3390/jof8030215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 01/27/2023] Open
Abstract
The ascomycetous fungus Ophiostoma novo-ulmi is the causative agent of the current Dutch elm disease (DED) pandemic, which has ravaged many tens of millions of European and North American elm trees. Host responses in vascular traits were studied in two Dutch elm hybrids, 'Groeneveld' and 'Dodoens', which show different vascular architecture in the secondary xylem and possess contrasting tolerances to DED. 'Groeneveld' trees, sensitive to DED, possessed a high number of small earlywood vessels. However, these trees showed a poor response to DED infection for the earlywood vascular characteristics. Following infection, the proportion of least vessels with a vessel lumen area less than 2500 µm2 decreased from 65.4% down to 53.2%. A delayed response in the increasing density of vessels showing a reduced size in the latewood prevented neither the rapid fungal spread nor the massive colonisation of the secondary xylem tissues resulting in the death of the infected trees. 'Dodoens' trees, tolerant to DED, possessed a low number of large earlywood vessels and showed a prominent and fast response to DED infection. Vessel lumen areas of newly formed earlywood vessels were severely reduced together with the vessel size : number ratio. Following infection, the proportion of least vessels with a vessel lumen area less than 2500 µm2 increased from 75.6% up to 92.9%. A trend in the increasing density of vessels showing a reduced size was maintained not only in the latewood that was formed in the year of infection but also in the earlywood that was formed in the consecutive year. The occurrence of fungal hyphae in the earlywood vessels that were formed a year following the infection was severely restricted, as revealed by X-ray micro-computed tomography imaging. Possible reasons responsible for a contrasting survival of 'Groeneveld' and 'Dodoens' trees are discussed.
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Affiliation(s)
- Michal Moravčík
- Department of Phytology, Technical University in Zvolen, T.G. Masaryka 24, 96001 Zvolen, Slovakia; (M.M.); (J.K.)
- Department of Pesticide Registration, ÚKSÚP Bratislava, SNP 99, 96202 Vígľaš, Slovakia
| | - Miroslava Mamoňová
- Department of Wood Science, Technical University in Zvolen, T.G. Masaryka 24, 96001 Zvolen, Slovakia; (M.M.); (V.R.)
| | - Vladimír Račko
- Department of Wood Science, Technical University in Zvolen, T.G. Masaryka 24, 96001 Zvolen, Slovakia; (M.M.); (V.R.)
| | - Ján Kováč
- Department of Phytology, Technical University in Zvolen, T.G. Masaryka 24, 96001 Zvolen, Slovakia; (M.M.); (J.K.)
| | - Miloň Dvořák
- Department of Forest Protection and Wildlife Management, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic;
| | | | - Jaroslav Ďurkovič
- Department of Phytology, Technical University in Zvolen, T.G. Masaryka 24, 96001 Zvolen, Slovakia; (M.M.); (J.K.)
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8
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Islam MT, Coutin JF, Shukla M, Dhaliwal AK, Nigg M, Bernier L, Sherif SM, Saxena PK. Deciphering the Genome-Wide Transcriptomic Changes during Interactions of Resistant and Susceptible Genotypes of American Elm with Ophiostoma novo-ulmi. J Fungi (Basel) 2022; 8:120. [PMID: 35205874 PMCID: PMC8874831 DOI: 10.3390/jof8020120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/22/2022] [Indexed: 12/10/2022] Open
Abstract
Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (Onu), is a destructive disease of American elm (Ulmus americana L.). The molecular mechanisms of resistance and susceptibility against DED in American elm are still largely uncharacterized. In the present study, we performed a de novo transcriptome (RNA-sequencing; RNA-Seq) assembly of U. americana and compared the gene expression in a resistant genotype, 'Valley Forge', and a susceptible (S) elm genotype at 0 and 96 h post-inoculation of Onu. A total of 85,863 non-redundant unigenes were identified. Compared to the previously characterized U. minor transcriptome, U. americana has 35,290 similar and 55,499 unique genes. The transcriptomic variations between 'Valley Forge' and 'S' were found primarily in the photosynthesis and primary metabolism, which were highly upregulated in the susceptible genotype irrespective of the Onu inoculation. The resistance to DED was associated with the activation of RPM1-mediated effector-triggered immunity that was demonstrated by the upregulation of genes involved in the phenylpropanoids biosynthesis and PR genes. The most significantly enriched gene ontology (GO) terms in response to Onu were response to stimulus (GO:0006950), response to stress (GO:0050896), and secondary metabolic process (GO:0008152) in both genotypes. However, only in the resistant genotype, the defense response (GO:0006952) was among the topmost significantly enriched GO terms. Our findings revealed the molecular regulations of DED resistance and susceptibility and provide a platform for marker-assisted breeding of resistant American elm genotypes.
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Affiliation(s)
- Md Tabibul Islam
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA;
| | - Jose Freixas Coutin
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada; (J.F.C.); (M.S.); (A.K.D.)
| | - Mukund Shukla
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada; (J.F.C.); (M.S.); (A.K.D.)
| | - Amandeep Kaur Dhaliwal
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada; (J.F.C.); (M.S.); (A.K.D.)
| | - Martha Nigg
- Centre d’Étude de la Forêt, Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (L.B.)
| | - Louis Bernier
- Centre d’Étude de la Forêt, Université Laval, Québec, QC G1V 0A6, Canada; (M.N.); (L.B.)
| | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA;
| | - Praveen K. Saxena
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, Guelph, ON N1G 2W1, Canada; (J.F.C.); (M.S.); (A.K.D.)
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9
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Sarmiento-Villamil JL, de Oliveira TC, Naruzawa ES, Bernier L. An Efficient Strategy for Obtaining Mutants by Targeted Gene Deletion in Ophiostoma novo-ulmi. Front Microbiol 2021; 12:699783. [PMID: 34335533 PMCID: PMC8317267 DOI: 10.3389/fmicb.2021.699783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
The dimorphic fungus Ophiostoma novo-ulmi is the highly aggressive pathogen responsible for the current, highly destructive, pandemic of Dutch elm disease (DED). Genome and transcriptome analyses of this pathogen previously revealed that a large set of genes expressed during dimorphic transition were also potentially related to plant infection processes, which seem to be regulated by molecular mechanisms different from those described in other dimorphic pathogens. Then, O. novo-ulmi can be used as a representative species to study the lifestyle of dimorphic pathogenic fungi that are not shared by the "model species" Candida albicans and Ustilago maydis. In order to gain better knowledge of molecular aspects underlying infection process and symptom induction by dimorphic fungi that cause vascular wilt disease, we developed a high-throughput gene deletion protocol for O. novo-ulmi. The protocol is based on transforming a Δmus52 O. novo-ulmi mutant impaired for non-homologous end joining (NHEJ) as the recipient strain, and transforming this strain with the latest version of OSCAR plasmids. The latter are used for generating deletion constructs containing the toxin-coding Herpes simplex virus thymidine kinase (HSVtk) gene which prevents ectopic integration of the T-DNA in Ophiostoma DNA. The frequency of gene deletion by homologous recombination (HR) at the ade1 locus associated with purine nucleotide biosynthesis was up to 77.8% in the Δmus52 mutant compared to 2% in the wild-type (WT). To validate the high efficiency of our deletion gene methodology we deleted ade7, which also belongs to the purine nucleotide pathway, as well as bct2, ogf1, and opf2 which encode fungal binuclear transcription factors (TFs). The frequency of gene replacement by HR for these genes reached up to 94%. We expect that our methodology combining the use of NHEJ deficient strains and OSCAR plasmids will function with similar high efficiencies for other O. novo-ulmi genes and other filamentous fungi.
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Affiliation(s)
- Jorge Luis Sarmiento-Villamil
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Thais Campos de Oliveira
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Erika Sayuri Naruzawa
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
- Collège Communautaire du Nouveau-Brunswick, Réseau CCNB-INNOV, Grand Falls, NB, Canada
| | - Louis Bernier
- Centre d’Étude de la Forêt (CEF) and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
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Phylogenomic Analyses of Nucleotide-Sugar Biosynthetic and Interconverting Enzymes Illuminate Cell Wall Composition in Fungi. mBio 2021; 12:mBio.03540-20. [PMID: 33849982 PMCID: PMC8092308 DOI: 10.1128/mbio.03540-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fungi are an enormously successful eukaryotic lineage that has colonized every aerobic habitat on Earth. This spectacular expansion is reflected in the dynamism and diversity of the fungal cell wall, a matrix of polysaccharides and glycoproteins pivotal to fungal life history strategies and a major target in the development of antifungal compounds. Cell wall polysaccharides are typically synthesized by Leloir glycosyltransferases, enzymes that are notoriously difficult to characterize, but their nucleotide-sugar substrates are well known and provide the opportunity to inspect the monosaccharides available for incorporation into cell wall polysaccharides and glycoproteins. In this work, we have used phylogenomic analyses of the enzymatic pathways that synthesize and interconvert nucleotide-sugars to predict potential cell wall monosaccharide composition across 491 fungal taxa. The results show a complex evolutionary history of these cell wall enzyme pathways and, by association, of the fungal cell wall. In particular, we see a significant reduction in monosaccharide diversity during fungal evolution, most notably in the colonization of terrestrial habitats. However, monosaccharide distribution is also shown to be varied across later-diverging fungal lineages.IMPORTANCE This study provides new insights into the complex evolutionary history of the fungal cell wall. We analyzed fungal enzymes that convert sugars acquired from the environment into the diverse sugars that make up the fundamental building blocks of the cell wall. Species-specific profiles of these nucleotide-sugar interconverting (NSI) enzymes for 491 fungi demonstrated multiple losses and gains of NSI proteins, revealing the rich diversity of cell wall architecture across the kingdom. Pragmatically, because cell walls are essential to fungi, our observations of variation in sugar diversity have important implications for the development of antifungal compounds that target the sugar profiles of specific pathogens.
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12
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Gilbert SF. Evolutionary developmental biology and sustainability: A biology of resilience. Evol Dev 2021; 23:273-291. [PMID: 33400344 DOI: 10.1111/ede.12366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/26/2022]
Abstract
Evolutionary developmental biology, and especially ecological developmental biology, is essential for discussions of sustainability and the responses to global climate change. First, this paper explores examples of animals that have successfully altered their development to accommodate human-made changes to their environments. We next document the ability of global warming to disrupt the development of those organisms with temperature-dependent sex-determination or with phenologies coordinating that organism's development with those of other species. The thermotolerance of Homo sapiens is also related to key developmental factors concerning brain development and maintenance, and the development of corals, the keystone organisms of tropical reefs, is discussed in relation to global warming as well as to other anthropogenic changes. While teratogenic and endocrine-disrupting compounds are not discussed in this essay, the ability of glyphosate herbicides to block insect development is highlighted. Last, the paper discusses the need to creatively integrate developmental biology with ecological, political, religious, and economic perspectives, as the flourishing of contemporary species may require altering the ways that Western science has considered the categories of nature, culture, and self.
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Affiliation(s)
- Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, USA
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Kijpornyongpan T, Aime MC. Investigating the Smuts: Common Cues, Signaling Pathways, and the Role of MAT in Dimorphic Switching and Pathogenesis. J Fungi (Basel) 2020; 6:jof6040368. [PMID: 33339287 PMCID: PMC7766764 DOI: 10.3390/jof6040368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
The corn smut fungus Ustilago maydis serves as a model species for studying fungal dimorphism and its role in phytopathogenic development. The pathogen has two growth phases: a saprobic yeast phase and a pathogenic filamentous phase. Dimorphic transition of U. maydis involves complex processes of signal perception, mating, and cellular reprogramming. Recent advances in improvement of reference genomes, high-throughput sequencing and molecular genetics studies have been expanding research in this field. However, the biology of other non-model species is frequently overlooked. This leads to uncertainty regarding how much of what is known in U. maydis is applicable to other dimorphic fungi. In this review, we will discuss dimorphic fungi in the aspects of physiology, reproductive biology, genomics, and molecular genetics. We also perform comparative analyses between U. maydis and other fungi in Ustilaginomycotina, the subphylum to which U. maydis belongs. We find that lipid/hydrophobicity is a potential common cue for dimorphic transition in plant-associated dimorphic fungi. However, genomic profiles alone are not adequate to explain dimorphism across different fungi.
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Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria. mSphere 2020; 5:5/5/e00737-20. [PMID: 33055257 PMCID: PMC7565894 DOI: 10.1128/msphere.00737-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. Emerging fungal pathogens are a threat to forest and agroecosystems, as well as animal and human health. How pathogens evolve from nonpathogenic ancestors is still poorly understood, making the prediction of future outbreaks challenging. Most pathogens have evolved lifestyle adaptations, which were enabled by specific changes in the gene content of the species. Hence, understanding transitions in the functions encoded by genomes gives valuable insight into the evolution of pathogenicity. Here, we studied lifestyle evolution in the genus Cryphonectria, including the prominent invasive pathogen Cryphonectria parasitica, the causal agent of chestnut blight on Castanea species. We assembled and compared the genomes of pathogenic and putatively nonpathogenic Cryphonectria species, as well as sister group pathogens in the family Cryphonectriaceae (Diaporthales, Ascomycetes), to investigate the evolution of genome size and gene content. We found a striking loss of genes associated with carbohydrate metabolism (CAZymes) in C. parasitica compared to other Cryphonectriaceae. Despite substantial CAZyme gene loss, experimental data suggest that C. parasitica has retained wood colonization abilities shared with other Cryphonectria species. Putative effectors substantially varied in number, cysteine content, and protein length among species. In contrast, secondary metabolite gene clusters show a high degree of conservation within the genus. Overall, our results underpin the recent lifestyle transition of C. parasitica toward a more pathogenic lifestyle. Our findings suggest that a CAZyme loss may have promoted pathogenicity of C. parasitica on Castanea species. Analyzing gene complements underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens. IMPORTANCE Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic repertoire enabling the colonization and exploitation of host species. Here, we have assembled >100 genomes across two related genera to identify key genomic determinants leading to the emergence of chestnut blight. We found subtle yet highly specific changes in the transition from saprotrophy to latent pathogenicity mostly determined by enzymes involved in carbohydrate metabolism. Large-scale genomic analyses of genes underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens.
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15
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Dort EN, Tanguay P, Hamelin RC. CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology. FRONTIERS IN PLANT SCIENCE 2020; 11:1126. [PMID: 32793272 PMCID: PMC7387688 DOI: 10.3389/fpls.2020.01126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/08/2020] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas9 gene editing technology has taken the scientific community by storm since its development in 2012. First discovered in 1987, CRISPR/Cas systems act as an adaptive immune response in archaea and bacteria that defends against invading bacteriophages and plasmids. CRISPR/Cas9 gene editing technology modifies this immune response to function in eukaryotic cells as a highly specific, RNA-guided complex that can edit almost any genetic target. This technology has applications in all biological fields, including plant pathology. However, examples of its use in forest pathology are essentially nonexistent. The aim of this review is to give researchers a deeper understanding of the native CRISPR/Cas systems and how they were adapted into the CRISPR/Cas9 technology used today in plant pathology-this information is crucial for researchers aiming to use this technology in the pathosystems they study. We review the current applications of CRISPR/Cas9 in plant pathology and propose future directions for research in forest pathosystems where this technology is currently underutilized.
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Affiliation(s)
- Erika N. Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada
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Iwanicki NS, Júnior ID, Eilenberg J, De Fine Licht HH. Comparative RNAseq Analysis of the Insect-Pathogenic Fungus Metarhizium anisopliae Reveals Specific Transcriptome Signatures of Filamentous and Yeast-Like Development. G3 (BETHESDA, MD.) 2020; 10:2141-2157. [PMID: 32354703 PMCID: PMC7341153 DOI: 10.1534/g3.120.401040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/24/2020] [Indexed: 11/18/2022]
Abstract
The fungus Metarhizium anisopliae is a facultative insect pathogen used as biological control agent of several agricultural pests worldwide. It is a dimorphic fungus that is able to display two growth morphologies, a filamentous phase with formation of hyphae and a yeast-like phase with formation of single-celled blastospores. Blastospores play an important role for M. anisopliae pathogenicity during disease development. They are formed solely in the hemolymph of infected insects as a fungal strategy to quickly multiply and colonize the insect's body. Here, we use comparative genome-wide transcriptome analyses to determine changes in gene expression between the filamentous and blastospore growth phases in vitro to characterize physiological changes and metabolic signatures associated with M. anisopliae dimorphism. Our results show a clear molecular distinction between the blastospore and mycelial phases. In total 6.4% (n = 696) out of 10,981 predicted genes in M. anisopliae were differentially expressed between the two phases with a fold-change > 4. The main physiological processes associated with up-regulated gene content in the single-celled yeast-like blastospores during liquid fermentation were oxidative stress, amino acid metabolism (catabolism and anabolism), respiration processes, transmembrane transport and production of secondary metabolites. In contrast, the up-regulated gene content in hyphae were associated with increased growth, metabolism and cell wall re-organization, which underlines the specific functions and altered growth morphology of M. anisopliae blastospores and hyphae, respectively. Our study revealed significant transcriptomic differences between the metabolism of blastospores and hyphae. These findings illustrate important aspects of fungal morphogenesis in M. anisopliae and highlight the main metabolic activities of each propagule under in vitro growth conditions.
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Affiliation(s)
- Natasha Sant'Anna Iwanicki
- Department of Entomology and Acarology, ESALQ- University of São Paulo, Av Padua Dias, 11-P.O. Box 9-13418-900, Piracicaba, SP, Brazil and
| | - Italo Delalibera Júnior
- Department of Entomology and Acarology, ESALQ- University of São Paulo, Av Padua Dias, 11-P.O. Box 9-13418-900, Piracicaba, SP, Brazil and
| | - Jørgen Eilenberg
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Henrik H De Fine Licht
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Hybridization and introgression drive genome evolution of Dutch elm disease pathogens. Nat Ecol Evol 2020; 4:626-638. [PMID: 32123324 DOI: 10.1038/s41559-020-1133-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022]
Abstract
Hybridization and the resulting introgression can drive the success of invasive species via the rapid acquisition of adaptive traits. The Dutch elm disease pandemics in the past 100 years were caused by three fungal lineages with permeable reproductive barriers: Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana. Using whole-genome sequences and growth phenotyping of a worldwide collection of isolates, we show that introgression has been the main driver of genomic diversity and that it impacted fitness-related traits. Introgressions contain genes involved in host-pathogen interactions and reproduction. Introgressed isolates have enhanced growth rate at high temperature and produce different necrosis sizes on an in vivo model for pathogenicity. In addition, lineages diverge in many pathogenicity-associated genes and exhibit differential mycelial growth in the presence of a proxy of a host defence compound, implying an important role of host trees in the molecular and functional differentiation of these pathogens.
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Rodriguez L, Voorhies M, Gilmore S, Beyhan S, Myint A, Sil A. Opposing signaling pathways regulate morphology in response to temperature in the fungal pathogen Histoplasma capsulatum. PLoS Biol 2019; 17:e3000168. [PMID: 31568523 PMCID: PMC6786654 DOI: 10.1371/journal.pbio.3000168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/10/2019] [Accepted: 09/04/2019] [Indexed: 12/24/2022] Open
Abstract
Phenotypic switching between 2 opposing cellular states is a fundamental aspect of biology, and fungi provide facile systems to analyze the interactions between regulons that control this type of switch. A long-standing mystery in fungal pathogens of humans is how thermally dimorphic fungi switch their developmental form in response to temperature. These fungi, including the subject of this study, Histoplasma capsulatum, are temperature-responsive organisms that utilize unknown regulatory pathways to couple their cell shape and associated attributes to the temperature of their environment. H. capsulatum grows as a multicellular hypha in the soil that switches to a pathogenic yeast form in response to the temperature of a mammalian host. These states can be triggered in the laboratory simply by growing the fungus either at room temperature (RT; which promotes hyphal growth) or at 37 °C (which promotes yeast-phase growth). Prior worked revealed that 15% to 20% of transcripts are differentially expressed in response to temperature, but it is unclear which transcripts are linked to specific phenotypic changes, such as cell morphology or virulence. To elucidate temperature-responsive regulons, we previously identified 4 transcription factors (required for yeast-phase growth [Ryp]1-4) that are required for yeast-phase growth at 37 °C; in each ryp mutant, the fungus grows constitutively as hyphae regardless of temperature, and the cells fail to express genes that are normally induced in response to growth at 37 °C. Here, we perform the first genetic screen to identify genes required for hyphal growth of H. capsulatum at RT and find that disruption of the signaling mucin MSB2 results in a yeast-locked phenotype. RNA sequencing (RNAseq) experiments reveal that MSB2 is not required for the majority of gene expression changes that occur when cells are shifted to RT. However, a small subset of temperature-responsive genes is dependent on MSB2 for its expression, thereby implicating these genes in the process of filamentation. Disruption or knockdown of an Msb2-dependent mitogen-activated protein (MAP) kinase (HOG2) and an APSES transcription factor (STU1) prevents hyphal growth at RT, validating that the Msb2 regulon contains genes that control filamentation. Notably, the Msb2 regulon shows conserved hyphal-specific expression in other dimorphic fungi, suggesting that this work defines a small set of genes that are likely to be conserved regulators and effectors of filamentation in multiple fungi. In contrast, a few yeast-specific transcripts, including virulence factors that are normally expressed only at 37 °C, are inappropriately expressed at RT in the msb2 mutant, suggesting that expression of these genes is coupled to growth in the yeast form rather than to temperature. Finally, we find that the yeast-promoting transcription factor Ryp3 associates with the MSB2 promoter and inhibits MSB2 transcript expression at 37 °C, whereas Msb2 inhibits accumulation of Ryp transcripts and proteins at RT. These findings indicate that the Ryp and Msb2 circuits antagonize each other in a temperature-dependent manner, thereby allowing temperature to govern cell shape and gene expression in this ubiquitous fungal pathogen of humans.
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Affiliation(s)
- Lauren Rodriguez
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Sarah Gilmore
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Sinem Beyhan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Anthony Myint
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Thakur MP, van der Putten WH, Cobben MMP, van Kleunen M, Geisen S. Microbial invasions in terrestrial ecosystems. Nat Rev Microbiol 2019; 17:621-631. [DOI: 10.1038/s41579-019-0236-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2019] [Indexed: 01/08/2023]
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20
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Cale JA, Klutsch JG, Dykstra CB, Peters B, Erbilgin N. Pathophysiological responses of pine defensive metabolites largely lack differences between pine species but vary with eliciting ophiostomatoid fungal species. TREE PHYSIOLOGY 2019; 39:1121-1135. [PMID: 30877758 DOI: 10.1093/treephys/tpz012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Phytopathogenic ophiostomatoid fungi are common associates of bark beetles and contribute to beetle-associated mortality of trees. Mountain pine beetle outbreaks in Canada are facilitating novel associations between its vectored fungi (Grosmannia clavigera, Leptographium longiclavatum and Ophiostoma montium) and jack pine. How the induced defense-related metabolite responses of jack and lodgepole pines vary in response to the fungi is unknown. Understanding this variation is important to clarifying pine susceptibility to and the physiological impacts of infection. We used a comparative metabolite profiling approach to investigate the defense-related signaling, carbon utilization/mobilization, and synthesis responses of both pines to the fungi. Both pine species largely exhibited similar metabolite responses to the fungi. The magnitude of pine metabolite responses positively reflected pathogen virulence. Our findings indicate that pines can recognize and metabolomically respond to novel pathogens, likely due to signals common between the novel fungi and fungi coevolved with the pine. Thus, jack pine is likely as susceptible as lodgepole pine to infections by each of the MPB-vectored fungi. Furthermore, the magnitude of the metabolite responses of both pines varied by the eliciting fungal species, with the most virulent pathogen causing the greatest reduction in carbohydrates and the highest accumulation of defensive terpenes.
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Affiliation(s)
- Jonathan A Cale
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Jennifer G Klutsch
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Christien B Dykstra
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Brosnon Peters
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, Canada
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21
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Ibarra Caballero JR, Jeon J, Lee YH, Fraedrich S, Klopfenstein NB, Kim MS, Stewart JE. Genomic comparisons of the laurel wilt pathogen, Raffaelea lauricola, and related tree pathogens highlight an arsenal of pathogenicity related genes. Fungal Genet Biol 2019; 125:84-92. [PMID: 30716558 DOI: 10.1016/j.fgb.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/09/2019] [Accepted: 01/31/2019] [Indexed: 12/15/2022]
Abstract
Raffaelea lauricola is an invasive fungal pathogen and symbiont of the redbay ambrosia beetle (Xyleborus glabratus) that has caused widespread mortality to redbay (Persea borbonia) and other Lauraceae species in the southeastern USA. We compare two genomes of R. lauricola (C2646 and RL570) to seven other related Ophiostomatales species including R. aguacate (nonpathogenic close relative of R. lauricola), R. quercus-mongolicae (associated with mortality of oaks in Korea), R. quercivora (associated with mortality of oaks in Japan), Grosmannia clavigera (cause of blue stain in conifers), Ophiostoma novo-ulmi (extremely virulent causal agent of Dutch elm disease), O. ulmi (moderately virulent pathogen that cause of Dutch elm disease), and O. piceae (blue-stain saprophyte of conifer logs and lumber). Structural and functional annotations were performed to determine genes that are potentially associated with disease development. Raffaelea lauricola and R. aguacate had the largest genomes, along with the largest number of protein-coding genes, genes encoding secreted proteins, small-secreted proteins, ABC transporters, cytochrome P450 enzymes, CAZYmes, and proteases. Our results indicate that this large genome size was not related to pathogenicity but was likely lineage specific, as the other pathogens in Raffaelea (R. quercus-mongolicae and R. quercivora) had similar genome characteristics to the Ophiostoma species. A diverse repertoire of wood-decaying enzymes were identified in each of the genomes, likely used for toxin neutralization rather than wood degradation. Lastly, a larger number of species-specific, secondary metabolite, synthesis clusters were identified in R. lauricola suggesting that it is well equipped as a pathogen, which could explain its success as a pathogen of a wide range of lauraceous hosts.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Stephen Fraedrich
- USDA Forest Service, Southern Research Station, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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22
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Abboud TG, Zubaer A, Wai A, Hausner G. The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. Can J Microbiol 2018; 64:339-348. [DOI: 10.1139/cjm-2017-0605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.
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Affiliation(s)
- Talal George Abboud
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Abdullah Zubaer
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alvan Wai
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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23
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Pita P, Rodríguez-Calcerrada J, Medel D, Gil L. Further insights into the components of resistance to Ophiostoma novo-ulmi in Ulmus minor: hydraulic conductance, stomatal sensitivity and bark dehydration. TREE PHYSIOLOGY 2018; 38:252-262. [PMID: 29040781 DOI: 10.1093/treephys/tpx123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Dutch elm disease (DED) is a vascular disease that has killed over 1 billion elm trees. The pathogen spreads throughout the xylem network triggering vessel blockage, which results in water stress, tissue dehydration and extensive leaf wilting in susceptible genotypes. We investigated the differences between four Ulmus minor Mill. clones of contrasting susceptibility to Ophiostoma novo-ulmi Brasier regarding morphological, anatomical and physiological traits affecting water transport, in order to gain a better understanding of the mechanisms underlying DED susceptibility. We analyzed the differential response to water shortage and increased air vapor pressure deficit (VPD) to investigate whether resistance to water stress might be related to DED tolerance. Sixteen plants per clone, aged 2 years, were grown inside a greenhouse under differential watering. Stomatal conductance was measured under ambient and increased VPD. Growth, bark water content and stem hydraulic and anatomical parameters were measured 22 days after starting differential watering. Vessel lumen area, lumen fraction and hydraulic conductance were highest in susceptible clones. Stomatal conductance was lowest under low VPD and decreased faster under increased VPD in resistant clones. We found a negative relationship between the decrease in stomatal conductance at increased VPD and specific hydraulic conductance, revealing a narrower hydraulic margin for sustaining transpiration in resistant clones. The effect of water shortage was greater on radial stem growth than on leaf area, which could be explained through an extensive use of capacitance water to buffer xylem water potential. Water shortage reduced stomatal conductance and vessel lumen area. Bark water content under conditions of water shortage only decreased in susceptible clones. Higher hydraulic constraints to sap flow in resistant clones may determine higher stomatal sensitivity to VPD and so contribute to DED resistance by limiting pathogen expansion and reducing water loss and metabolic impairment in cells involved in fighting against infection.
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Affiliation(s)
- Pilar Pita
- ETSI Montes, Forestal y del Medio Natural, Dep. Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Jesús Rodríguez-Calcerrada
- ETSI Montes, Forestal y del Medio Natural, Dep. Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - David Medel
- ETSI Montes, Forestal y del Medio Natural, Dep. Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Luis Gil
- ETSI Montes, Forestal y del Medio Natural, Dep. Sistemas y Recursos Naturales, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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24
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Wingfield BD, Berger DK, Steenkamp ET, Lim HJ, Duong TA, Bluhm BH, de Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier N, Lin YC, Van de Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, van der Nest MA, van der Merwe NA, van Wyk S, Wilken PM, Wingfield MJ. IMA Genome-F 8: Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus 2017; 8:385-396. [PMID: 29242781 PMCID: PMC5729718 DOI: 10.5598/imafungus.2017.08.02.10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/09/2017] [Indexed: 11/29/2022] Open
Abstract
The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces. The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Dave K. Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Hye-Jin Lim
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Burton H. Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, USA
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - G. Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Nicky Olivier
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Yao-Cheng Lin
- VIB Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- VIB Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Bridget G. Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicole Soal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Catherine Tatham
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Stephanie van Wyk
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
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25
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Schuelke TA, Wu G, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes MD. Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia. Genome Biol Evol 2017; 9:3312-3327. [PMID: 29186370 PMCID: PMC5737690 DOI: 10.1093/gbe/evx242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2017] [Indexed: 12/29/2022] Open
Abstract
Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vectored into the host via the walnut twig beetle. Geosmithia morbida was first detected in western United States and currently threatens the timber industry concentrated in eastern United States. We sequenced the genomes of G. morbida in a previous study and two nonpathogenic Geosmithia species in this work and compared these species to other fungal pathogens and nonpathogens to identify genes under positive selection in G. morbida that may be associated with pathogenicity. Geosmithia morbida possesses one of the smallest genomes among the fungal species observed in this study, and one of the smallest fungal pathogen genomes to date. The enzymatic profile in this pathogen is very similar to its nonpathogenic relatives. Our findings indicate that genome reduction or retention of a smaller genome may be an important adaptative force during the evolution of a specialized lifestyle in fungal species that occupy a specificniche, such as beetle vectored tree pathogens. We also present potential genes under selection in G. morbida that could be important for adaptation to a pathogenic lifestyle.
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Affiliation(s)
- Taruna A Schuelke
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
| | - Guangxi Wu
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
| | | | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University
| | - David C Plachetzki
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
| | - Matthew D MacManes
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
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26
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Vanderpool D, Bracewell RR, McCutcheon JP. Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars. Mol Ecol 2017; 27:2077-2094. [PMID: 29087025 DOI: 10.1111/mec.14394] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/05/2017] [Accepted: 10/11/2017] [Indexed: 12/27/2022]
Abstract
Bark and ambrosia beetles are highly specialized weevils (Curculionidae) that have established diverse symbioses with fungi, most often from the order Ophiostomatales (Ascomycota, Sordariomycetes). The two types of beetles are distinguished by their feeding habits and intimacy of interactions with their symbiotic fungi. The tree tissue diet of bark beetles is facilitated by fungi, while ambrosia beetles feed solely on fungi that they farm. The farming life history strategy requires domestication of a fungus, which the beetles consume as their sole food source. Ambrosia beetles in the subfamily Platypodinae originated in the mid-Cretaceous (119-88 Ma) and are the oldest known group of farming insects. However, attempts to resolve phylogenetic relationships and the timing of domestication events for fungal cultivars have been largely inconclusive. We sequenced the genomes of 12 ambrosia beetle fungal cultivars and bark beetle associates, including the devastating laurel wilt pathogen, Raffaelea lauricola, to estimate a robust phylogeny of the Ophiostomatales. We find evidence for contemporaneous diversification of the beetles and their associated fungi, followed by three independent domestication events of the ambrosia fungi genus Raffaelea. We estimate the first domestication of an Ophiostomatales fungus occurred ~86 Ma, 25 million years earlier than prior estimates and in close agreement with the estimated age of farming in the Platypodinae (96 Ma). Comparisons of the timing of fungal domestication events with the timing of beetle radiations support the hypothesis that the first large beetle radiations may have spread domesticated "ambrosia" fungi to other fungi-associated beetle groups, perhaps facilitating the evolution of new farming lineages.
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Affiliation(s)
- Dan Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Ryan R Bracewell
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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27
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Wilken PM, Steenkamp ET, Wingfield MJ, de Beer ZW, Wingfield BD. Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Sbaraini N, Andreis FC, Thompson CE, Guedes RLM, Junges Â, Campos T, Staats CC, Vainstein MH, Ribeiro de Vasconcelos AT, Schrank A. Genome-Wide Analysis of Secondary Metabolite Gene Clusters in O phiostoma ulmi and Ophiostoma novo-ulmi Reveals a Fujikurin-Like Gene Cluster with a Putative Role in Infection. Front Microbiol 2017; 8:1063. [PMID: 28659888 PMCID: PMC5468452 DOI: 10.3389/fmicb.2017.01063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/29/2017] [Indexed: 01/08/2023] Open
Abstract
The emergence of new microbial pathogens can result in destructive outbreaks, since their hosts have limited resistance and pathogens may be excessively aggressive. Described as the major ecological incident of the twentieth century, Dutch elm disease, caused by ascomycete fungi from the Ophiostoma genus, has caused a significant decline in elm tree populations (Ulmus sp.) in North America and Europe. Genome sequencing of the two main causative agents of Dutch elm disease (Ophiostoma ulmi and Ophiostoma novo-ulmi), along with closely related species with different lifestyles, allows for unique comparisons to be made to identify how pathogens and virulence determinants have emerged. Among several established virulence determinants, secondary metabolites (SMs) have been suggested to play significant roles during phytopathogen infection. Interestingly, the secondary metabolism of Dutch elm pathogens remains almost unexplored, and little is known about how SM biosynthetic genes are organized in these species. To better understand the metabolic potential of O. ulmi and O. novo-ulmi, we performed a deep survey and description of SM biosynthetic gene clusters (BGCs) in these species and assessed their conservation among eight species from the Ophiostomataceae family. Among 19 identified BGCs, a fujikurin-like gene cluster (OpPKS8) was unique to Dutch elm pathogens. Phylogenetic analysis revealed that orthologs for this gene cluster are widespread among phytopathogens and plant-associated fungi, suggesting that OpPKS8 may have been horizontally acquired by the Ophiostoma genus. Moreover, the detailed identification of several BGCs paves the way for future in-depth research and supports the potential impact of secondary metabolism on Ophiostoma genus’ lifestyle.
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Affiliation(s)
- Nicolau Sbaraini
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Fábio C Andreis
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Claudia E Thompson
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Rafael L M Guedes
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Ângela Junges
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Thais Campos
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Charley C Staats
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Marilene H Vainstein
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Ana T Ribeiro de Vasconcelos
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Laboratório Nacional de Computação CientíficaPetrópolis, Brazil
| | - Augusto Schrank
- Rede Avançada em Biologia ComputacionalPetrópolis, Brazil.,Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
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29
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Lah L, Löber U, Hsiang T, Hartmann S. A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles. Fungal Biol 2016; 121:234-252. [PMID: 28215351 DOI: 10.1016/j.funbio.2016.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 12/10/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022]
Abstract
Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.
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Affiliation(s)
- Ljerka Lah
- Evolutionary Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | - Ulrike Löber
- Evolutionary Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, N1G 2W1 Guelph, ON, Canada
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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30
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Nigg M, Bernier L. From yeast to hypha: defining transcriptomic signatures of the morphological switch in the dimorphic fungal pathogen Ophiostoma novo-ulmi. BMC Genomics 2016; 17:920. [PMID: 27846799 PMCID: PMC5111228 DOI: 10.1186/s12864-016-3251-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/03/2016] [Indexed: 12/19/2022] Open
Abstract
Background Yeast-to-hypha transition is a major morphological change in fungi. Molecular regulators and pathways that are involved in this process have been extensively studied in model species, including Saccharomyces cerevisiae. The Mitogen-Actived Protein Kinase (MAPK) cascade, for example, is known to be involved in the yeast-to-pseudohypha switch. Yet the conservation of mechanisms regulating such morphological changes in non-model fungi is still poorly understood. Here, we investigate cell remodeling and transcriptomic modifications that occur during this morphological switch in the highly aggressive ascomycete fungus Ophiostoma novo-ulmi, the causal agent of Dutch elm disease. Results Using a combination of light microscopy, scanning electron microscopy and flow cytometry, we demonstrate that the morphological switch occurs in less than 27 h, with phenotypic cell modifications being detected within the first 4 h. Using RNAseq, we found that over 22% of the genome of O. novo-ulmi is differentially expressed during the transition. By performing clustering analyses of time series gene expression data, we identified several sets of genes that are differentially expressed according to distinct and representative temporal profiles. Further, we found that several genes that are homologous to S. cerevisiae MAPK genes are regulated during the yeast-to-hypha transition in O. novo-ulmi and mostly over-expressed, suggesting convergence in gene expression regulation. Conclusions Our results are the first report of a time-course experiment monitoring the morphological transition in a non-model Sordariomycota species and reveal many genes of interest for further functional investigations of fungal dimorphism. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3251-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M Nigg
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Room 2255, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada. .,Département des sciences du bois et de la forêt, Centre d'Étude de la Forêt (CEF), Université Laval, Québec, G1V 0A6, Canada.
| | - L Bernier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Room 2255, Pavillon Charles-Eugène-Marchand, 1030, Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada.,Département des sciences du bois et de la forêt, Centre d'Étude de la Forêt (CEF), Université Laval, Québec, G1V 0A6, Canada
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31
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Aylward J, Steenkamp ET, Dreyer LL, Roets F, Wingfield MJ, Wingfield BD. Genetic basis for high population diversity in Protea-associated Knoxdaviesia. Fungal Genet Biol 2016; 96:47-57. [DOI: 10.1016/j.fgb.2016.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 11/25/2022]
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Wadke N, Kandasamy D, Vogel H, Lah L, Wingfield BD, Paetz C, Wright LP, Gershenzon J, Hammerbacher A. The Bark-Beetle-Associated Fungus, Endoconidiophora polonica, Utilizes the Phenolic Defense Compounds of Its Host as a Carbon Source. PLANT PHYSIOLOGY 2016; 171:914-31. [PMID: 27208235 PMCID: PMC4902585 DOI: 10.1104/pp.15.01916] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
Norway spruce (Picea abies) is periodically attacked by the bark beetle Ips typographus and its fungal associate, Endoconidiophora polonica, whose infection is thought to be required for successful beetle attack. Norway spruce produces terpenoid resins and phenolics in response to fungal and bark beetle invasion. However, how the fungal associate copes with these chemical defenses is still unclear. In this study, we investigated changes in the phenolic content of Norway spruce bark upon E. polonica infection and the biochemical factors mediating these changes. Although genes encoding the rate-limiting enzymes in Norway spruce stilbene and flavonoid biosynthesis were actively transcribed during fungal infection, there was a significant time-dependent decline of the corresponding metabolites in fungal lesions. In vitro feeding experiments with pure phenolics revealed that E. polonica transforms both stilbenes and flavonoids to muconoid-type ring-cleavage products, which are likely the first steps in the degradation of spruce defenses to substrates that can enter the tricarboxylic acid cycle. Four genes were identified in E. polonica that encode catechol dioxygenases carrying out these reactions. These enzymes catalyze the cleavage of phenolic rings with a vicinal dihydroxyl group to muconoid products accepting a wide range of Norway spruce-produced phenolics as substrates. The expression of these genes and E. polonica utilization of the most abundant spruce phenolics as carbon sources both correlated positively with fungal virulence in several strains. Thus, the pathways for the degradation of phenolic compounds in E. polonica, initiated by catechol dioxygenase action, are important to the infection, growth, and survival of this bark beetle-vectored fungus and may play a major role in the ability of I. typographus to colonize spruce trees.
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Affiliation(s)
- Namita Wadke
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Dineshkumar Kandasamy
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Ljerka Lah
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Brenda D Wingfield
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Christian Paetz
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Louwrance P Wright
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
| | - Almuth Hammerbacher
- Max Planck Institute for Chemical Ecology, 07745 Jena, Germany (N.W., D.K., H.V., C.P., L.P.W., J.G., A.H.);University of Potsdam, 14476 Golm, Germany (L.L.); andDepartment of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa (B.D.W.)
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Haueisen J, Stukenbrock EH. Life cycle specialization of filamentous pathogens - colonization and reproduction in plant tissues. Curr Opin Microbiol 2016; 32:31-37. [PMID: 27153045 DOI: 10.1016/j.mib.2016.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/31/2022]
Abstract
Filamentous plant pathogens explore host tissues to obtain nutrients for growth and reproduction. Diverse strategies for tissue invasion, defense manipulation, and colonization of inter and intra-cellular spaces have evolved. Most research has focused on effector molecules, which are secreted to manipulate plant immunity and facilitate infection. Effector genes are often found to evolve rapidly in response to the antagonistic host-pathogen co-evolution but other traits are also subject to adaptive evolution during specialization to the anatomy, biochemistry and ecology of different plant hosts. Although not directly related to virulence, these traits are important components of specialization but little is known about them. We present and discuss specific life cycle traits that facilitate exploration of plant tissues and underline the importance of increasing our insight into the biology of plant pathogens.
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Affiliation(s)
- Janine Haueisen
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany; Christian-Albrechts University Kiel, Am Botanischen Garten 1-11, 24118 Kiel, Germany
| | - Eva H Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany; Christian-Albrechts University Kiel, Am Botanischen Garten 1-11, 24118 Kiel, Germany.
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Mating type markers reveal high levels of heterothallism in Leptographium sensu lato. Fungal Biol 2016; 120:538-546. [PMID: 27020155 DOI: 10.1016/j.funbio.2016.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 01/16/2023]
Abstract
Species of Leptographium sensu lato are sap-stain fungi vectored by bark beetles and some species cause or are associated with tree diseases. Sexual states have been reported for more than 30 species in this group and these have been treated in the sexual genus Grosmannia. No sexual state is known for at least 59 additional species and these reside in the genus Leptographium. The discovery of sexual states for species of Leptographium relies mainly on the presence of fruiting bodies on host tissue at the time of isolation and/or intensive laboratory mating studies, which commonly have low levels of success. We developed mating-type markers to study sexual compatibility of species in Leptographium sensu lato. Using these markers, it was possible to identify mating types for 42 species and to determine thallism in many species for the first time. Surprisingly, the results showed that heterothallic and putatively heterothallic species are abundant (39 out of 42 species) in Leptographium sensu lato, and only three species were confirmed to be homothallic. The mating type markers developed in this study will be useful for future studies concerning mating type and sexual compatibility of species in this genus.
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35
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Sherif SM, Shukla MR, Murch SJ, Bernier L, Saxena PK. Simultaneous induction of jasmonic acid and disease-responsive genes signifies tolerance of American elm to Dutch elm disease. Sci Rep 2016; 6:21934. [PMID: 26902398 PMCID: PMC4763294 DOI: 10.1038/srep21934] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/03/2016] [Indexed: 01/07/2023] Open
Abstract
Dutch elm disease (DED), caused by three fungal species in the genus Ophiostoma, is the most devastating disease of both native European and North American elm trees. Although many tolerant cultivars have been identified and released, the tolerance mechanisms are not well understood and true resistance has not yet been achieved. Here we show that the expression of disease-responsive genes in reactions leading to tolerance or susceptibility is significantly differentiated within the first 144 hours post-inoculation (hpi). Analysis of the levels of endogenous plant defense molecules such as jasmonic acid (JA) and salicylic acid (SA) in tolerant and susceptible American elm saplings suggested SA and methyl-jasmonate as potential defense response elicitors, which was further confirmed by field observations. However, the tolerant phenotype can be best characterized by a concurrent induction of JA and disease-responsive genes at 96 hpi. Molecular investigations indicated that the expression of fungal genes (i.e. cerato ulmin) was also modulated by endogenous SA and JA and this response was unique among aggressive and non-aggressive fungal strains. The present study not only provides better understanding of tolerance mechanisms to DED, but also represents a first, verified template for examining simultaneous transcriptomic changes during American elm-fungus interactions.
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Affiliation(s)
- S. M. Sherif
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada,Department of Horticulture, Faculty of Agriculture, Damanhour University, Al-Gomhuria St., PO Box 22516, Damanhour, Al-Behira, Egypt
| | - M. R. Shukla
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - S. J. Murch
- Chemistry Department, University of British Columbia, Kelowna, BC, Canada
| | - L. Bernier
- Centre d’étude de la forêt (CEF) and Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - P. K. Saxena
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada,
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36
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de Sain M, Rep M. The Role of Pathogen-Secreted Proteins in Fungal Vascular Wilt Diseases. Int J Mol Sci 2015; 16:23970-93. [PMID: 26473835 PMCID: PMC4632733 DOI: 10.3390/ijms161023970] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 01/07/2023] Open
Abstract
A limited number of fungi can cause wilting disease in plants through colonization of the vascular system, the most well-known being Verticillium dahliae and Fusarium oxysporum. Like all pathogenic microorganisms, vascular wilt fungi secrete proteins during host colonization. Whole-genome sequencing and proteomics screens have identified many of these proteins, including small, usually cysteine-rich proteins, necrosis-inducing proteins and enzymes. Gene deletion experiments have provided evidence that some of these proteins are required for pathogenicity, while the role of other secreted proteins remains enigmatic. On the other hand, the plant immune system can recognize some secreted proteins or their actions, resulting in disease resistance. We give an overview of proteins currently known to be secreted by vascular wilt fungi and discuss their role in pathogenicity and plant immunity.
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Affiliation(s)
- Mara de Sain
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands.
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098XH, The Netherlands.
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37
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RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi. G3-GENES GENOMES GENETICS 2015; 5:2487-95. [PMID: 26384770 PMCID: PMC4632067 DOI: 10.1534/g3.115.021022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fungal dimorphism is a complex trait and our understanding of the ability of fungi to display different growth morphologies is limited to a small number of model species. Here we study a highly aggressive dimorphic fungus, the ascomycete Ophiostoma novo-ulmi, which is a model in plant pathology and the causal agent of Dutch elm disease. The two growth phases that this fungus displays, i.e., a yeast phase and mycelial phase, are thought to be involved in key steps of disease development. We used RNAseq to investigate the genome-wide gene expression profiles that are associated with yeast and mycelial growth phases in vitro. Our results show a clear molecular distinction between yeast and mycelial phase gene expression profiles. Almost 12% of the gene content is differentially expressed between the two phases, which reveals specific functions related to each growth phase. We compared O. novo-ulmi transcriptome profiles with those of two model dimorphic fungi, Candida albicans and Histoplasma capsulatum. Few orthologs showed similar expression regulation between the two growth phases, which suggests that, globally, the genes associated with these two life forms are poorly conserved. This poor conservation underscores the importance of developing specific tools for emerging model species that are distantly related to the classical ones. Taken together, our results provide insights into transcriptome regulation and molecular specificity in O. novo-ulmi and offer a new perspective for understanding fungal dimorphism.
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Perdiguero P, Venturas M, Cervera MT, Gil L, Collada C. Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease. FRONTIERS IN PLANT SCIENCE 2015; 6:541. [PMID: 26257751 PMCID: PMC4507047 DOI: 10.3389/fpls.2015.00541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/03/2015] [Indexed: 05/30/2023]
Abstract
Elms, especially Ulmus minor and U. americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to single nucleotide polymorphisms (SNPs; 27,359). In a subset randomly selected for validation, 87% of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.
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Affiliation(s)
- Pedro Perdiguero
- Grupo de Investigación en Genética, Fisiología e Historia Forestal, Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Universidad Politécnica de MadridMadrid, Spain
| | - Martin Venturas
- Grupo de Investigación en Genética, Fisiología e Historia Forestal, Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de MadridMadrid, Spain
| | - María Teresa Cervera
- Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Universidad Politécnica de MadridMadrid, Spain
- Departamento de Ecología y Genética, Centro de Investigación Forestal, Instituto Nacional de Investigación y Tecnología Agraria y AlimentariaMadrid, Spain
| | - Luis Gil
- Grupo de Investigación en Genética, Fisiología e Historia Forestal, Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Universidad Politécnica de MadridMadrid, Spain
| | - Carmen Collada
- Grupo de Investigación en Genética, Fisiología e Historia Forestal, Departamento de Sistemas y Recursos Naturales, Universidad Politécnica de MadridMadrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Universidad Politécnica de MadridMadrid, Spain
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Wingfield BD, Ades PK, Al-Naemi FA, Beirn LA, Bihon W, Crouch JA, de Beer ZW, De Vos L, Duong TA, Fields CJ, Fourie G, Kanzi AM, Malapi-Wight M, Pethybridge SJ, Radwan O, Rendon G, Slippers B, Santana QC, Steenkamp ET, Taylor PW, Vaghefi N, van der Merwe NA, Veltri D, Wingfield MJ. IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata. IMA Fungus 2015; 6:233-48. [PMID: 26203426 PMCID: PMC4500086 DOI: 10.5598/imafungus.2015.06.01.15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 12/15/2022] Open
Abstract
The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Peter K. Ades
- Department of Forest and Ecosystem Science, The University of Melbourne, Victoria, 3010, Australia
| | - Fatima A. Al-Naemi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Lisa A. Beirn
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Wubetu Bihon
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
- Agricultural Research Council, Vegetable and Ornamental Plant Institute, P. Bag X293, Pretoria 0001, South Africa
| | - Jo Anne Crouch
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Christopher J. Fields
- High Performance Biological Computing Group, Roy J. Carver Biotechnology Center/W.M. Keck Center, University of Illinois at Urbana-Champaign, IL, USA
| | - Gerda Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Aquillah M. Kanzi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Martha Malapi-Wight
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
| | - Sarah J. Pethybridge
- School of Integrative Plant Sciences, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Osman Radwan
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, IL, USA and Department of Plant Production, College of Technology, Zagazig University, Sharkia, Egypt
| | - Gloria Rendon
- High Performance Biological Computing Group, Roy J. Carver Biotechnology Center/W.M. Keck Center, University of Illinois at Urbana-Champaign, IL, USA
| | - Bernard Slippers
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Quentin C. Santana
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
| | - Paul W.J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, 3010, Australia
| | - Niloofar Vaghefi
- School of Integrative Plant Sciences, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Daniel Veltri
- Systematic Mycology and Microbiology Laboratory, U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Beltsville, MD 20705, USA
- Oak Ridge Laboratories ARS Research Participation Program, USDA-ARS, Beltsville, MD 20705, USA
| | - Michael J. Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. bag x20, Pretoria 0028, South Africa
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Dai L, Li Z, Yu J, Ma M, Zhang R, Chen H, Pham T. The CYP51F1 Gene of Leptographium qinlingensis: Sequence Characteristic, Phylogeny and Transcript Levels. Int J Mol Sci 2015; 16:12014-34. [PMID: 26016505 PMCID: PMC4490426 DOI: 10.3390/ijms160612014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/04/2015] [Indexed: 11/16/2022] Open
Abstract
Leptographium qinlingensis is a fungal associate of the Chinese white pine beetle (Dendroctonus armandi) and a pathogen of the Chinese white pine (Pinus armandi) that must overcome the terpenoid oleoresin defenses of host trees. L. qinlingensis responds to monoterpene flow with abundant mechanisms that include export and the use of these compounds as a carbon source. As one of the fungal cytochrome P450 proteins (CYPs), which play important roles in general metabolism, CYP51 (lanosterol 14-α demethylase) can catalyze the biosynthesis of ergosterol and is a target for antifungal drug. We have identified an L. qinlingensis CYP51F1 gene, and the phylogenetic analysis shows the highest homology with the 14-α-demethylase sequence from Grosmannia clavigera (a fungal associate of Dendroctonus ponderosae). The transcription level of CYP51F1 following treatment with terpenes and pine phloem extracts was upregulated, while using monoterpenes as the only carbon source led to the downregulation of CYP5F1 expression. The homology modeling structure of CYP51F1 is similar to the structure of the lanosterol 14-α demethylase protein of Saccharomyces cerevisiae YJM789, which has an N-terminal membrane helix 1 (MH1) and transmembrane helix 1 (TMH1). The minimal inhibitory concentrations (MIC) of terpenoid and azole fungicides (itraconazole (ITC)) and the docking of terpenoid molecules, lanosterol and ITC in the protein structure suggested that CYP51F1 may be inhibited by terpenoid molecules by competitive binding with azole fungicides.
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Affiliation(s)
- Lulu Dai
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Zhumei Li
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Jiamin Yu
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Mingyuan Ma
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Ranran Zhang
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Hui Chen
- College of Forestry, Northwest A&F University, Yangling 712100, China.
| | - Thanh Pham
- College of Forestry, Northwest A&F University, Yangling 712100, China.
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