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

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 new 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 4–5 possible horizontal transfers to other mu..., , , # Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

***

Data set contains:

=====Assembly\_graphs.zip=====
Assembly graph outputs from SPades genome assembly in .gfa format. These asseembly graphs were used as input for the DNA barcode extraction using PATHRacer (see methods for paramaters).

=====Assembly\_scaffolds.zip=====
Assembled genome assembly scaffolds from SPades. These draft metagenome assemblies where used for down stream phylogenetic analysis and protein preductions (see methods for paramaters).

=====Protein\_predictions\_of\_Psilocybin\_producing\_taxa.zip=====
Protein predictions in GFF format for pislocybin-producing taxa. Proteins predections were perfomred on bioinformatically reduced genomes (from diploid to haploid) using Redundands. Profiles were generated using the Program Augustus (see methods for paramaters).

=====Raw\_phylogenetic\_trees.zip=====

==Mega11\_calibration\_tests==
Time divergenc...