Phylogenomics, divergence times and notes of orders in Basidiomycota

He, Mao‑Qiang and Cao, Bin and Liu, Fei and Boekhout, Teun and Denchev, Teodor T. and Schoutteten, Nathan and Denchev, Cvetomir M. and Kemler, Martin and Gorjón, Sergio P. and Begerow, Dominik and Valenzuela, Ricardo and Davoodian, Naveed and Niskanen, Tuula and Vizzini, Alfredo and Redhead, Scott A. and Ramírez‑Cruz, Virginia and Papp, Viktor and Dudka, Vasiliy A. and Dutta, Arun Kumar and García‑Sandoval, Ricardo and Liu, Xin‑Zhan and Kijpornyongpan, Teeratas and Savchenko, Anton and Tedersoo, Leho and Theelen, Bart and Trierveiler‑Pereira, Larissa and Wu, Fang and Carlos Zamora, Juan and Zeng, Xiang‑Yu and Zhou, Li‑Wei and Liu, Shi‑Liang and Ghobad‑Nejhad, Masoomeh and Giachini, Admir J. and Li, Guo‑Jie and Kakishima, Makoto and Olariaga, Ibai and Haelewaters, Danny and Sulistyo, Bobby and Sugiyama, Junta and Svantesson, Sten and Yurkov, Andrey and Alvarado, Pablo and Antonín, Vladimír and da Silva, André Felipe and Druzhinina, Irina and Gibertoni, Tatiana B. and Guzmán‑Dávalos, Laura and Justo, Alfredo and Karunarathna, Samantha C. and Galappaththi, Mahesh C. A. and Toome‑Heller, Merje and Hosoya, Tsuyoshi and Liimatainen, Kare and Márquez, Rodrigo and Mešić, Armin and Moncalvo, Jean‑Marc and Nagy, László G. and Varga, Torda and Orihara, Takamichi and Raymundo, Tania and Salcedo, Isabel and Silva‑Filho, Alexandre G. S. and Tkalčec, Zdenko and Wartchow, Felipe and Zhao, Chang‑Lin and Bau, Tolgor and Cabarroi‑Hernández, Milay and Cortés‑Pérez, Alonso and Decock, Cony and De Lange, Ruben and Weiss, Michael and Menolli Jr., Nelson and Nilsson, R. Henrik and Fan, Yu‑Guang and Verbeken, Annemieke and Gaforov, Yusufon and Meiras‑Ottoni, Angelina and Mendes‑Alvarenga, Renato L. and Zeng, Nian‑Kai and Wu, Qi and Hyde, Kevin D. and Kirk, Paul M. and Zhao, Rui‑Lin (2024) Phylogenomics, divergence times and notes of orders in Basidiomycota. Fungal Diversity, 126. 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, defning characteristics, evolution, justifcation of orders, problems, signifcance, 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 identifcation and classifcation, however, has become increasingly challenging.

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