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Bradshaw AJ, Ramírez-Cruz V, Awan AR, Furci G, Guzmán-Dávalos L, Dentinger BTM. Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster. Proc Natl Acad Sci U S A 2024; 121:e2311245121. [PMID: 38194448 PMCID: PMC10801892 DOI: 10.1073/pnas.2311245121] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.
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Affiliation(s)
- Alexander J. Bradshaw
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
| | - Virginia Ramírez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Ali R. Awan
- Genomics Innovation Unit, Guy’s and St.Thomas’ NHS Foundation Trust, St Thomas’ Hospital, LondonSE1 7EH, United Kingdom
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan45147, Mexico
| | - Bryn T. M. Dentinger
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112
- Natural History Museum of Utah, Collections and Research, University of Utah, Salt Lake City, UT84108
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McTaggart AR, McLaughlin S, Slot JC, McKernan K, Appleyard C, Bartlett TL, Weinert M, Barlow C, Warne LN, Shuey LS, Drenth A, James TY. Domestication through clandestine cultivation constrained genetic diversity in magic mushrooms relative to naturalized populations. Curr Biol 2023; 33:5147-5159.e7. [PMID: 38052161 DOI: 10.1016/j.cub.2023.10.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/04/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023]
Abstract
Fungi that are edible or fermentative were domesticated through selective cultivation of their desired traits. Domestication is often associated with inbreeding or selfing, which may fix traits other than those under selection, and causes an overall decrease in heterozygosity. A hallucinogenic mushroom, Psilocybe cubensis, was domesticated from its niche in livestock dung for production of psilocybin. It has caused accidental poisonings since the 1940s in Australia, which is a population hypothesized to be introduced from an unknown center of origin. We sequenced genomes of 38 isolates from Australia and compared them with 86 genomes of commercially available cultivars to determine (1) whether P. cubensis was introduced to Australia, and (2) how domestication has impacted commercial cultivars. Our analyses of genome-wide SNPs and single-copy orthologs showed that the Australian population is naturalized, having recovered its effective population size after a bottleneck when it was introduced, and it has maintained relatively high genetic diversity based on measures of nucleotide and allelic diversity. In contrast, domesticated cultivars generally have low effective population sizes and hallmarks of selfing and clonal propagation, including low genetic diversity, low heterozygosity, high linkage disequilibrium, and low allelic diversity of mating-compatibility genes. Analyses of kinship show that most cultivars are founded from related populations. Alleles in the psilocybin gene cluster are identical across most cultivars of P. cubensis with low diversity across coding sequence; however, unique allelic diversity in Australia and some cultivars may translate to differences in biosynthesis of psilocybin and its analogs.
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Affiliation(s)
- Alistair R McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; Funky Fungus, Burpengary, QLD 4505, Australia.
| | | | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Kevin McKernan
- Research and Development, Medicinal Genomics, Beverly, MA 01915, USA
| | | | - Tia L Bartlett
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Matthew Weinert
- Entheogenesis Australis, PO Box 2046, Belgrave, 3160 VIC, Australia
| | - Caine Barlow
- Entheogenesis Australis, PO Box 2046, Belgrave, 3160 VIC, Australia
| | - Leon N Warne
- Little Green Pharma, West Perth, WA 6005, Australia
| | - Louise S Shuey
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - André Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48104, USA
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Miller DR, Jacobs JT, Rockefeller A, Singer H, Bollinger IM, Conway J, Slot JC, Cliffel DE. Cultivation, chemistry, and genome of Psilocybe zapotecorum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.564784. [PMID: 37961470 PMCID: PMC10635036 DOI: 10.1101/2023.11.01.564784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Psilocybe zapotecorum is a strongly blue-bruising psilocybin mushroom used by indigenous groups in southeastern Mexico and beyond. While this species has a rich history of ceremonial use, research into its chemistry and genetics have been limited. Herein, we detail mushroom morphology and report on cultivation parameters, chemical profile, and the full genome sequence of P. zapotecorum . First, growth and cloning methods are detailed that are simple, and reproducible. In combination with high resolution microscopic analysis, the strain was barcoded, confirming species-level identification. Full genome sequencing reveals the architecture of the psilocybin gene cluster in P. zapotecorum, and can serve as a reference genome for Psilocybe Clade I. Characterization of the tryptamine profile revealed a psilocybin concentration of 17.9±1.7 mg/g, with a range of 10.6-25.7 mg/g (n=7), and similar tryptamines (psilocin, baeocystin, norbaeocystin, norpsilocin, aeruginascin, 4-HO-tryptamine, and tryptamine) in lesser concentrations for a combined tryptamine concentration of 22.5±3.2 mg/g. These results show P. zapotecorum to be a potent - and variable - Psilocybe mushroom. Chemical profiling, genetic analysis, and cultivation assist in demystifying these mushrooms. As clinical studies with psilocybin gain traction, understanding the diversity of psilocybin mushrooms will assure that psilocybin therapy does not become synonymous with psilocybin mushrooms.
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