He, M.-Q. and Cao, B. and Liu, F. and Boekhout, T. and Denchev, T.T. and Schoutteten, N. and Denchev, C.M. and Kemler, M. and Gorjón, S.P. and Begerow, D. and Valenzuela, R. and Davoodian, N. and Niskanen, T. and Vizzini, A. and Redhead, S.A. and Ramírez-Cruz, V. and Papp, Viktor and Dudka, V.A. and Dutta, A.K. and García-Sandoval, R. and Liu, X.-Z. and Kijpornyongpan, T. and Savchenko, A. and Tedersoo, L. and Theelen, B. and Trierveiler-Pereira, L. and Wu, F. and Zamora, J.C. and Zeng, X.-Y. and Zhou, L.-W. and Nagy, László and Varga, Torda (2024) Phylogenomics, divergence times and notes of orders in Basidiomycota. FUNGAL DIVERSITY, 126 (1). pp. 127-406. ISSN 1560-2745
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Abstract
Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outline of Basidiomycota based on the phylogenomic relationships and the taxonomic studies since 2019; and we provide notes for each order and discuss the history, defining characteristics, evolution, justification of orders, problems, significance, and plates. Our phylogenomic analysis suggests that the subphyla diverged in a time range of 443–490 Myr (million years), classes in a time range of 312–412 Myr, and orders in a time range of 102–361 Myr. Families diverged in a time range of 50–289 Myr, 76–224 Myr, and 62–156 Myr in Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina, respectively. Based on the phylogenomic relationships and divergence times, we propose a new suborder Mycenineae in Agaricales to accommodate Mycenaceae. In the current outline of Basidiomycota, there are four subphyla, 20 classes, 77 orders, 297 families, and 2134 genera accepted. When building a robust taxonomy of Basidiomycota in the genomic era, the generation of molecular phylogenetic data has become relatively easier. Finding phenotypical characters, especially those that can be applied for identification and classification, however, has become increasingly challenging. © The Author(s) under exclusive licence to Mushroom Research Foundation 2024.
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| Additional Information: | State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China The Yeasts Foundation, Amsterdam, Netherlands Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin St., Sofia, 1113, Bulgaria IUCN SSC Rusts and Smuts Specialist Group, Sofia, Bulgaria Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium Institute of Plant Science and Microbiology, Organismic Botany and Mycology, Universität Hamburg, Ohnhorststr. 18, Hamburg, 22609, Germany Department of Botany and Plant Physiology, Plant DNA-Biobank, University of Salamanca, C/ Licenciado Méndez Nieto s/n, Salamanca, 37007, Spain Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Plan de Ayala y Carpio s/n, Santo Tomás, Del. Miguel Hidalgo, Mexico, CP 11340, Mexico Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia Fungal Diversity and Systematics Team, Royal Botanic Gardens, Surrey, Kew, TW9 3AB, United Kingdom Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O.Box 7, Helsinki, 00014, Finland Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, Turin, 10125, Italy Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R., Viale P.A. Mattioli, 25, Turin, 10125, Italy National Mycological Herbarium/DAOM, Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, 960 Carling Ave., William Saunders Building (Bldg. 49), Ottawa, ON K1A0C6, Canada University of Guadalajara, postal 1–139, Jalisco, Apdo., Zapopan, 45147, Mexico Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, 1518, Hungary Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov Str. 2, St Petersburg, 197376, Russian Federation Yugra State University, Chekhova str. 16, Khanty-Mansi Autonomous Okrug – Yugra, Khanty-Mansiysk, 628012, Russian Federation Molecular & amp; Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Assam, Guwahati, 781014, India Facultad de Ciencias, Universidad Nacional Autónoma de México, Av Universidad 3000, Mexico, CP 04510, Mexico Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia Mycology and Microbiology Center, University of Tartu, Tartu, Estonia College of Science, King Saud University, Riyadh, Saudi Arabia Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, Netherlands Centro de Ciências da Natureza, Universidade Federal de São Carlos, Campus Lagoa do Sino, SP, Buri, Brazil Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China Conservatoire et Jardin Botaniques de Genève, Chemin de l’Impératrice 1, Chambésy, Geneva, 1292, Switzerland Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, China Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran, 3353136846, Iran Department of Microbiology, Universidade Federal de Santa Catarina, SC, Florianópolis, 88040-900, Brazil College of Horticulture, Hebei Agricultural University, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Baoding, China University of Tsukuba, Ibaraki, Tsukuba, 305-8572, Japan Biology and Geology, Physics and Inorganic Chemistry Department, Rey Juan Carlos University, C/Tulipán s/n, Móstoles, Madrid, 28933, Spain Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic Centro de Investigaciones Micológicas (CIMi), Facultad de Ciencias Naturales y Exactes, Universidad Autónoma de Chiriquí, David, Apartado Postal 0427, Panama Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Ibaraki, Tsukuba, 305-0005, Japan TechnoSuruga Laboratory Co., Ltd., 388-1, Shizuoka, Nagasaki, 424-0065, Japan Department of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, Göteborg, 405 30, Sweden Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Brunswick, 38124, Germany ALVALAB, Dr. Fernando Bongera st., Severo Ochoa bldg. S1.04, Oviedo, 33006, Spain Department of Botany, Moravian Museum, Zelný Trh 6, Brno, 659 37, Czech Republic Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Recife, Brazil New Brunswick Museum, Saint John, NB E2K 1E5, Canada Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Yunnan, Qujing, China National Institute of Fundamental Studies (NIFS), Hantana Road, Kandy, Sri Lanka Harry Butler Institute, Murdoch University, Perth, WA 6150, Australia Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, 1072, New Zealand Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, 10000, Croatia Department of Ecology & amp; Evolutionary Biology, and Royal Ontario Museum, University of Toronto, Toronto, ON M5S 2C6, Canada Synthetic and Systems Biology Unit, Biological Research Center, HUN-REN, Szeged, 6726, Hungary Comparative Fungal Biology, Royal Botanic Gardens, Richmond, Kew, TW9 3AB, United Kingdom Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Kanagawa, Odawara, 250-0031, Japan Department of Plant Biology and Ecology (Botany), University of the Basque Country (UPV/EHU), Apdo 644, Bilbao, 48080, Spain Department of Natural Sciences and Mathematics (DCM), IFungiLab, Federal Institute of Education, Science and Technology of São Paulo (IFSP), Subarea of Biology (SAB), Campus São Paulo (SPO), Rua Pedro Vicente, 625, Sao Paulo, 01109-010, Brazil Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Campus I, PB, João Pessoa, Brazil College of Biodiversity Conservation, Southwest Forestry University, Yunnan, Kunming, 650224, China Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China Mycothèque de l’Université Catholique de Louvain (BCCM/MUCL), Croix du Sud 2 bte L5.06.07, Louvain-la-Neuve, 1348, Belgium Organismal Mycology and Microbiology, Steinbeis Innovation Center, Vor dem Kreuzberg 17, Tübingen, 72070, Germany Department of Biology, University of Tübingen, Auf der Morgenstelle 26, Tübingen, 72076, Germany Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Hainan, Haikou, 571199, China New Uzbekistan University, 54 Mustaqillik Ave., Tashkent, 100007, Uzbekistan Central Asian University, 264 Milliy Bog Street, Tashkent, 111221, Uzbekistan Mycology Laboratory, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, 32 Durmon Yuli, Tashkent, 100125, Uzbekistan Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Hainan, Haikou, 571158, China Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, Kunming, 650201, China Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225, China College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 100408, China Cited By :7 Export Date: 27 November 2024 Correspondence Address: Zhao, R.-L.; State Key Laboratory of Mycology, China; email: zhaorl@im.ac.cn |
| Uncontrolled Keywords: | Classification, Fungi, Molecular clock, Systematics, Taxonomy |
| Subjects: | Q Science / természettudomány > QH Natural history / természetrajz > QH301 Biology / biológia S Agriculture / mezőgazdaság > SB Plant culture / növénytermesztés > SB976.F85 Fungi / gombák |
| SWORD Depositor: | MTMT SWORD |
| Depositing User: | MTMT SWORD |
| Date Deposited: | 27 Jan 2025 09:58 |
| Last Modified: | 27 Jan 2025 09:58 |
| URI: | https://real.mtak.hu/id/eprint/214381 |
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