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 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.