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Phylogenomics, divergence times and notes of orders in Basidiomycota

Mao-Qiang He, Bin Cao, Fei Liu, Teun Boekhout, Teodor T. Denchev, Nathan Schoutteten (UGent) , Cvetomir M. Denchev, Martin Kemler, Sergio P. Gorjon, Dominik Begerow, et al.
(2024) FUNGAL DIVERSITY. 126(1). p.1-125
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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.
Keywords
MUSHROOM-FORMING FUNGI, NUCLEAR LARGE SUBUNIT, COMB. NOV CRYPTOBASIDIACEAE, HIGHER-LEVEL CLASSIFICATION, RIBOSOMAL DNA-SEQUENCES, WOOD DECAY MECHANISMS, WHITE-ROT FUNGI, PHYLOGENETIC-RELATIONSHIPS, SP.-NOV., GEN. NOV., Classification, Fungi, Molecular clock, Systematics, Taxonomy

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Citation

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MLA
He, Mao-Qiang, et al. “Phylogenomics, Divergence Times and Notes of Orders in Basidiomycota.” FUNGAL DIVERSITY, vol. 126, no. 1, 2024, pp. 1–125, doi:10.1007/s13225-024-00535-w.
APA
He, M.-Q., Cao, B., Liu, F., Boekhout, T., Denchev, T. T., Schoutteten, N., … Zhao, R.-L. (2024). Phylogenomics, divergence times and notes of orders in Basidiomycota. FUNGAL DIVERSITY, 126(1), 1–125. https://doi.org/10.1007/s13225-024-00535-w
Chicago author-date
He, Mao-Qiang, Bin Cao, Fei Liu, Teun Boekhout, Teodor T. Denchev, Nathan Schoutteten, Cvetomir M. Denchev, et al. 2024. “Phylogenomics, Divergence Times and Notes of Orders in Basidiomycota.” FUNGAL DIVERSITY 126 (1): 1–125. https://doi.org/10.1007/s13225-024-00535-w.
Chicago author-date (all authors)
He, Mao-Qiang, Bin Cao, Fei Liu, Teun Boekhout, Teodor T. Denchev, Nathan Schoutteten, Cvetomir M. Denchev, Martin Kemler, Sergio P. Gorjon, Dominik Begerow, Ricardo Valenzuela, Naveed Davoodian, Tuula Niskanen, Alfredo Vizzini, Scott A. Redhead, Virginia Ramirez-Cruz, Viktor Papp, Vasiliy A. Dudka, Arun Kumar Dutta, Ricardo Garcia-Sandoval, Xin-Zhan Liu, Teeratas Kijpornyongpan, Anton Savchenko, Leho Tedersoo, Bart Theelen, Larissa Trierveiler-Pereira, Fang Wu, Juan Carlos Zamora, Xiang-Yu Zeng, Li-Wei Zhou, Shi-Liang Liu, Masoomeh Ghobad-Nejhad, Admir J. Giachini, Guo-Jie Li, Makoto Kakishima, Ibai Olariaga, Danny Haelewaters, Bobby Sulistyo, Junta Sugiyama, Sten Svantesson, Andrey Yurkov, Pablo Alvarado, Vladimir Antonin, Andre Felipe da Silva, Irina Druzhinina, Tatiana B. Gibertoni, Laura Guzman-Davalos, Alfredo Justo, Samantha C. Karunarathna, Mahesh C. A. Galappaththi, Merje Toome-Heller, Tsuyoshi Hosoya, Kare Liimatainen, Rodrigo Marquez, Armin Mesic, Jean-Marc Moncalvo, Laszlo G. Nagy, Torda Varga, Takamichi Orihara, Tania Raymundo, Isabel Salcedo, Alexandre G. S. Silva-Filho, Zdenko Tkalcec, Felipe Wartchow, Chang-Lin Zhao, Tolgor Bau, Milay Cabarroi-Hernandez, Alonso Cortes-Perez, Cony Decock, Ruben De Lange, Michael Weiss, Nelson Menolli Jr, R. Henrik Nilsson, Yu-Guang Fan, Annemieke Verbeken, Yusufjon Gafforov, Angelina Meiras-Ottoni, Renato L. Mendes-Alvarenga, Nian-Kai Zeng, Qi Wu, Kevin D. Hyde, Paul M. Kirk, and Rui-Lin Zhao. 2024. “Phylogenomics, Divergence Times and Notes of Orders in Basidiomycota.” FUNGAL DIVERSITY 126 (1): 1–125. doi:10.1007/s13225-024-00535-w.
Vancouver
1.
He M-Q, Cao B, Liu F, Boekhout T, Denchev TT, Schoutteten N, et al. Phylogenomics, divergence times and notes of orders in Basidiomycota. FUNGAL DIVERSITY. 2024;126(1):1–125.
IEEE
[1]
M.-Q. He et al., “Phylogenomics, divergence times and notes of orders in Basidiomycota,” FUNGAL DIVERSITY, vol. 126, no. 1, pp. 1–125, 2024.
@article{01J4M3Q85M4F0JKA01E9RGEGN9,
  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.}},
  author       = {{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  Gorjon, Sergio P. and  Begerow, Dominik and  Valenzuela, Ricardo and  Davoodian, Naveed and  Niskanen, Tuula and  Vizzini, Alfredo and  Redhead, Scott A. and  Ramirez-Cruz, Virginia and  Papp, Viktor and  Dudka, Vasiliy A. and  Dutta, Arun Kumar and  Garcia-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  Zamora, Juan Carlos 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  Antonin, Vladimir and  da Silva, Andre Felipe and  Druzhinina, Irina and  Gibertoni, Tatiana B. and  Guzman-Davalos, Laura and  Justo, Alfredo and  Karunarathna, Samantha C. and  Galappaththi, Mahesh C. A. and  Toome-Heller, Merje and  Hosoya, Tsuyoshi and  Liimatainen, Kare and  Marquez, Rodrigo and  Mesic, Armin and  Moncalvo, Jean-Marc and  Nagy, Laszlo G. and  Varga, Torda and  Orihara, Takamichi and  Raymundo, Tania and  Salcedo, Isabel and  Silva-Filho, Alexandre G. S. and  Tkalcec, Zdenko and  Wartchow, Felipe and  Zhao, Chang-Lin and  Bau, Tolgor and  Cabarroi-Hernandez, Milay and  Cortes-Perez, 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  Gafforov, Yusufjon 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}},
  issn         = {{1560-2745}},
  journal      = {{FUNGAL DIVERSITY}},
  keywords     = {{MUSHROOM-FORMING FUNGI,NUCLEAR LARGE SUBUNIT,COMB. NOV CRYPTOBASIDIACEAE,HIGHER-LEVEL CLASSIFICATION,RIBOSOMAL DNA-SEQUENCES,WOOD DECAY MECHANISMS,WHITE-ROT FUNGI,PHYLOGENETIC-RELATIONSHIPS,SP.-NOV.,GEN. NOV.,Classification,Fungi,Molecular clock,Systematics,Taxonomy}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{1--125}},
  title        = {{Phylogenomics, divergence times and notes of orders in Basidiomycota}},
  url          = {{http://doi.org/10.1007/s13225-024-00535-w}},
  volume       = {{126}},
  year         = {{2024}},
}
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