Phylogenomics, divergence times and notes of orders in Basidiomycota
Por:
He M.-Q., Cao B., Liu F., Boekhout T., Denchev T.T., Schoutteten N., Denchev C.M., Kemler M., Gorjón S.P., Begerow D., Valenzuela R., Davoodian N., Niskanen T., Vizzini A., Redhead S.A., Ramírez-Cruz V., Papp V., Dudka V.A., Dutta A.K., García-Sandoval R., Liu X.-Z., Kijpornyongpan T., Savchenko A., Tedersoo L., Theelen B., Trierveiler-Pereira L., Wu F., Zamora J.C., Zeng X.-Y., Zhou L.-W., Liu S.-L., Ghobad-Nejhad M., Giachini A.J., Li G.-J., Kakishima M., Olariaga I., Haelewaters D., Sulistyo B., Sugiyama J., Svantesson S., Yurkov A., Alvarado P., Antonín V., da Silva A.F., Druzhinina I., Gibertoni T.B., Guzmán-Dávalos L., Justo A., Karunarathna S.C., Galappaththi M.C.A., Toome-Heller M., Hosoya T., Liimatainen K., Márquez R., Mešic A., Moncalvo J.-M., Nagy L.G., Varga T., Orihara T., Raymundo T., Salcedo I., Silva-Filho A.G.S., Tkalcec Z., Wartchow F., Zhao C.-L., Bau T., Cabarroi-Hernández M., Cortés-Pérez A., Decock C., De Lange R., Weiss M., Menolli N., Jr., Nilsson R.H., Fan Y.-G., Verbeken A., Gafforov Y., Meiras-Ottoni A., Mendes-Alvarenga R.L., Zeng N.-K., Wu Q., Hyde K.D., Kirk P.M., Zhao R.-L.
Publicada:
1 ene 2024
Ahead of Print:
1 jul 2024
Resumen:
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.
Filiaciones:
He M.-Q.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Cao B.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Liu F.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Boekhout T.:
The Yeasts Foundation, Amsterdam, Netherlands
Denchev T.T.:
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
Schoutteten N.:
Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium
Denchev C.M.:
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
Kemler M.:
IUCN SSC Rusts and Smuts Specialist Group, Sofia, Bulgaria
Institute of Plant Science and Microbiology, Organismic Botany and Mycology, Universität Hamburg, Ohnhorststr. 18, Hamburg, 22609, Germany
Gorjón S.P.:
Department of Botany and Plant Physiology, Plant DNA-Biobank, University of Salamanca, C/ Licenciado Méndez Nieto s/n, Salamanca, 37007, Spain
Begerow D.:
Institute of Plant Science and Microbiology, Organismic Botany and Mycology, Universität Hamburg, Ohnhorststr. 18, Hamburg, 22609, Germany
Valenzuela R.:
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
Davoodian N.:
Royal Botanic Gardens Victoria, Melbourne, 3004, VIC, Australia
Niskanen T.:
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
Vizzini A.:
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
Redhead S.A.:
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, K1A0C6, ON, Canada
Ramírez-Cruz V.:
University of Guadalajara, postal 1–139, Jalisco, Apdo., Zapopan, 45147, Mexico
Papp V.:
Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, 1518, Hungary
Dudka V.A.:
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
Dutta A.K.:
Molecular & amp
García-Sandoval R.:
Facultad de Ciencias, Universidad Nacional Autónoma de México, Av Universidad 3000, Mexico, CP 04510, Mexico
Liu X.-Z.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Kijpornyongpan T.:
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
Savchenko A.:
Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
Tedersoo L.:
Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
College of Science, King Saud University, Riyadh, Saudi Arabia
Theelen B.:
Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, Netherlands
Trierveiler-Pereira L.:
Centro de Ciências da Natureza, Universidade Federal de São Carlos, Campus Lagoa do Sino, SP, Buri, Brazil
Wu F.:
Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
Zamora J.C.:
Conservatoire et Jardin Botaniques de Genève, Chemin de l’Impératrice 1, Chambésy, Geneva, 1292, Switzerland
Zeng X.-Y.:
Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, China
Zhou L.-W.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Liu S.-L.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Ghobad-Nejhad M.:
Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 3353-5111, Tehran, 3353136846, Iran
Giachini A.J.:
Department of Microbiology, Universidade Federal de Santa Catarina, SC, Florianópolis, 88040-900, Brazil
Li G.-J.:
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
Kakishima M.:
University of Tsukuba, Ibaraki, Tsukuba, 305-8572, Japan
Olariaga I.:
Biology and Geology, Physics and Inorganic Chemistry Department, Rey Juan Carlos University, C/Tulipán s/n, Móstoles, Madrid, 28933, Spain
Haelewaters D.:
Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium
Faculty of Science, University of South Bohemia, Branišovská 31, Ceske Budejovice, 370 05, Czech Republic
Centro de Investigaciones Micológicas (CIMi), Facultad de Ciencias Naturales y Exactes, Universidad Autónoma de Chiriquí, David, Apartado Postal 0427, Panama
Sulistyo B.:
Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium
Sugiyama J.:
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
Svantesson S.:
Department of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
Laboratory for Biological Diversity, Ruder Boškovic Institute, Bijenicka cesta 54, Zagreb, 10000, Croatia
Yurkov A.:
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Brunswick, 38124, Germany
Alvarado P.:
ALVALAB, Dr. Fernando Bongera st., Severo Ochoa bldg. S1.04, Oviedo, 33006, Spain
Antonín V.:
Department of Botany, Moravian Museum, Zelný trh 6, Brno, 659 37, Czech Republic
da Silva A.F.:
Department of Microbiology, Universidade Federal de Santa Catarina, SC, Florianópolis, 88040-900, Brazil
Druzhinina I.:
Fungal Diversity and Systematics Team, Royal Botanic Gardens, Surrey, Kew, TW9 3AB, United Kingdom
Gibertoni T.B.:
Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Recife, Brazil
Guzmán-Dávalos L.:
University of Guadalajara, postal 1–139, Jalisco, Apdo., Zapopan, 45147, Mexico
Justo A.:
New Brunswick Museum, Saint John, E2K 1E5, NB, Canada
Karunarathna S.C.:
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
Galappaththi M.C.A.:
Harry Butler Institute, Murdoch University, Perth, 6150, WA, Australia
Toome-Heller M.:
Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, 1072, New Zealand
Hosoya T.:
Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Ibaraki, Tsukuba, 305-0005, Japan
Liimatainen K.:
Fungal Diversity and Systematics Team, Royal Botanic Gardens, Surrey, Kew, TW9 3AB, United Kingdom
Márquez R.:
Biology and Geology, Physics and Inorganic Chemistry Department, Rey Juan Carlos University, C/Tulipán s/n, Móstoles, Madrid, 28933, Spain
Mešic A.:
Laboratory for Biological Diversity, Ruder Boškovic Institute, Bijenicka cesta 54, Zagreb, 10000, Croatia
Moncalvo J.-M.:
Department of Ecology & amp
Nagy L.G.:
Synthetic and Systems Biology Unit, Biological Research Center, HUN-REN, Szeged, 6726, Hungary
Varga T.:
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
Orihara T.:
Kanagawa Prefectural Museum of Natural History, 499 Iryuda, Kanagawa, Odawara, 250-0031, Japan
Raymundo T.:
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
Salcedo I.:
Department of Plant Biology and Ecology (Botany), University of the Basque Country (UPV/EHU), Apdo 644, Bilbao, 48080, Spain
Silva-Filho A.G.S.:
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
Tkalcec Z.:
Laboratory for Biological Diversity, Ruder Boškovic Institute, Bijenicka cesta 54, Zagreb, 10000, Croatia
Wartchow F.:
Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Campus I, PB, João Pessoa, Brazil
Zhao C.-L.:
College of Biodiversity Conservation, Southwest Forestry University, Yunnan, Kunming, 650224, China
Bau T.:
Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, 130118, China
Cabarroi-Hernández M.:
University of Guadalajara, postal 1–139, Jalisco, Apdo., Zapopan, 45147, Mexico
Cortés-Pérez A.:
University of Guadalajara, postal 1–139, Jalisco, Apdo., Zapopan, 45147, Mexico
Decock C.:
Mycothèque de l’Université catholique de Louvain (BCCM/MUCL), Croix du Sud 2 bte L5.06.07, Louvain-la-Neuve, 1348, Belgium
De Lange R.:
Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium
Weiss M.:
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
Menolli N.:
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
Jr.:
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
Nilsson R.H.:
Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Box 461, Göteborg, 405 30, Sweden
Fan Y.-G.:
Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Hainan, Haikou, 571199, China
Verbeken A.:
Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Ghent, 9000, Belgium
Gafforov Y.:
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
Meiras-Ottoni A.:
Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Recife, Brazil
Mendes-Alvarenga R.L.:
Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Recife, Brazil
Zeng N.-K.:
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
Wu Q.:
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
Hyde K.D.:
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
Kirk P.M.:
Fungal Diversity and Systematics Team, Royal Botanic Gardens, Surrey, Kew, TW9 3AB, United Kingdom
Zhao R.-L.:
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, Huairou District, Beijing, 100408, China
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