A draft reference assembly of the Psilocybe cubensis genome

McKernan, Kevin; Kane, Liam T.; Crawford, Seth; Chin, Chen-Shan; Trippe, Aaron; McLaughlin, Stephen

doi:10.12688/f1000research.51613.2

Cited by 3 publications

(4 citation statements)

References 23 publications

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“…Psilocybin gene cluster detection was performed using the Augustus version 3.4.0 gene prediction software ( 91 ) with the flags –singlestrand=true to predict genes independently on each strand with the coprinus_cinereus training set. Following gene prediction, the most likely psilocybin BGC for each species was chosen as follows: Using the protein sequences for PsiD (tryptophan decarboxylase), PsiK (kinase), PsiM (methyltransferase), and PsiH (P450) based on the publicly available chromosomal level assembly for P. cubensis ( 92 ), we used BLASTP with default parameters to search for homologs in the predicted translated proteins for each species. The top three hits for each gene were then used together to find putative clusters by examining the gene numbers assigned by augustus.…”

Section: Methodsmentioning

confidence: 99%

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Bradshaw,

Ramírez-Cruz,

Awan

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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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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Section: Methodsmentioning

confidence: 99%

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Bradshaw,

Ramírez-Cruz,

Awan

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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show abstract

“…Psilocybin gene cluster detection was performed using the Augustus version 3.4.0 gene prediction software (Stanke et al 2006) with the flags -singlestrand=true to predict genes independently on each strand, and using the coprinus_cinereus training set. Following gene prediction, the most likely psilocybin BGC for each species was chosen as follows: using the protein sequences for PsiD, PsiK, PsiH, and PsiM based on the publicly available chromosomal level assembly for P. cubensis (McKernan et al 2021), we used BLASTP with default parameters to search for homologs in the predicted translated proteins for each species. The top three hits for each gene were then used together to find putative clusters by examining the gene numbers assigned by Augustus.…”

Section: Gene Prediction Of Psilocybin Gene Cluster and Construction ...mentioning

confidence: 99%

“…Phylogenetic analysis indicated that this cluster has been horizontally acquired by psilocybin-producing mushrooms in other genera with common ecological niches (Awan et al 2018; Reynolds et al 2018), although the direction and relative timing of these transfers remains unclear. Notably, only a select few species of Psilocybe have been investigated at a genomic scale (Fricke et al 2017; Awan et al 2018; Reynolds et al 2018; McKernan et al 2021; Dörner et al 2022), which does not represent all of the known ecologies, and they do not span the phylogenetic range of the two major clades identified by Ramírez-Cruz et al (2013a), severely limiting inferences of evolutionary patterns.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of the psychoactive mushroom genusPsilocybeand evolution of the psilocybin biosynthetic gene cluster

Bradshaw

Ramírez-Cruz

Awan

et al. 2022

Preprint

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Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite a recent surge in interest in these mushrooms due to emerging evidence that psilocybin, the main psychoactive compound, is a promising therapeutic for a variety of mental illnesses, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny for Psilocybe using shotgun sequencing of 71 fungarium specimens, including 23 types, and conducting phylogenomic analysis using 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage arose ~66 mya and diversified ~53 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4-5 possible horizontal transfers to other mushrooms between 40 and 22 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the cluster that corresponds to a deep split within the genus, possibly consistent with the independent acquisition of the cluster. This novel insight may predict differences in chemistry between the two major clades of the genus, providing further resources for the development of novel therapeutics.

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“…In this study, we analyze the difference between liquid culture and grain spawn substrate for mycelial colonization. Although the genome of P. cubensis has recently been drafted, with 32 contigs mapping 97.6% of the genome by benchmarking universal single-copy orthologs (BUSCO) completeness score ( McKernan et al., 2021 ), to date, no metabolomic mapping of Psilocybe spp. growth stages has been published.…”

Section: Introductionmentioning

confidence: 99%

Exploring Psilocybe spp. mycelium and fruiting body chemistry for potential therapeutic compounds

Waldbillig,

Baranova,

Neumann

et al. 2023

Front. Fungal Biol.

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Psilocybe mushrooms, otherwise known as “magic” mushrooms, owe their psychedelic effect to psilocin, a serotonin subtype 2A (5-HT2A) receptor agonist and metabolite of psilocybin, the primary indole alkaloid found in Psilocybe species. Metabolomics is an advanced fingerprinting tool that can be utilized to identify the differences among fungal life stages that may otherwise be unaccounted for. In this study, by using targeted and untargeted (metabolomic) multivariate analysis, we demonstrate that the chemical composition of Psilocybe differs among mycelia, grain mycelia, and fruiting bodies. The preferential accumulation of psilocybin, baeocystin, tryptophan, ergothioneine, and phenylethylamine in fruiting bodies differentiated them from mycelia; however, the levels of alpha-glycerylphosphorylcholine (α-GPC), N-acetylglucosamine, and trimethylglycine were found to be proportionally higher in mycelia than in fruiting bodies based on Pareto-scaled data. Considering the wealth of compounds with therapeutic potential that have been isolated from various fungal genera, it would be pertinent to study the compounds found in Psilocybe mycelia as potential naturally derived therapeutic targets.

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A draft reference assembly of the Psilocybe cubensis genome

Cited by 3 publications

References 23 publications

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Phylogenomics of the psychoactive mushroom genusPsilocybeand evolution of the psilocybin biosynthetic gene cluster

Exploring Psilocybe spp. mycelium and fruiting body chemistry for potential therapeutic compounds

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