Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster
Cite this dataset
Bradshaw, Alexander et al. (2023). Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster [Dataset]. Dryad. https://doi.org/10.5061/dryad.tmpg4f52s
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 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.
README: 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 divergence trees and mega analysis environments(see methods for paramaters)
=LSU tree=
Divergence analysis for LSU species tree
Multiple sequence alignment (mafft_alignment.fasta), gene tree output from iqtree (.tre), Mega11 tree output (.nwk), and full Mega11 sesion file (.MTSX).
=Psilocybe top100 tree=
Divergence analysis for the Psilocybe species tree
Multiple sequence alignment (mafft_alignment.fasta), gene tree output from iqtree (.tre), Mega11 tree output (.nwk), and full Mega11 sesion file (.MTSX).
==Phylogenomic_trees==
Unaltered phylogenetic trees for each analysis, main and supplementary (see methods for paramaters)
=Figure_2=
raw tree file output from iqtree for only the psilocybe species used in figure 2.
=Figure_3=
mafft sequence alignment and raw tree file output from iqtree for samples used in PsiD analysis in figure 3. Also Includes PDF files with full PsiD contig infromation, and with clean labels that only include sample name.
=constraint4=
Raw tree output from iqtree for psilocybe that was used as the constraint tree for all public barcode data found in supplementary figures.
==Psilocybin_cluster_gene_trees==
Mafft alignments used for each individual Psi cluster gene tree (see methods for paramaters).
Raw tree output from iqtree or each individual Psi cluster gene tree (see methods for paramaters).
PDF file with tip labels only presenting sample names.
==Supplementary figure phylogenetic trees==
=Alignments=
Mafft alignments used for each public barcode gene tree (see methods for paramaters).
=Trees=
Raw tree output for all supplementary figures (see methods for paramaters).
=====ASR.zip=====
Input and output data used for ansectral state reconstruction (ASR) (see methods for paramaters). Includes the input tree and states, as well as the alter output file to remove outgroups from the phylogenetic tree. Also includes the ASR outputs altered to be compatible with Tracer.
=====Supplementary_tables.zip=====
This directory contains supplementary tables 1-r
Supplementary Table 1: Voucher table of Specimens
Voucher table of all specimens sequenced and analyzed. Table include relevant voucher information, current name designation, and SRA and BioSample accession numbers.
Supplementary Table 2: Genome assembly and BUSCO stats for each specimen
Genome assembly statistics, and BUSCO complete gene recovery from the Agaricales_db10 database.
Tab 1: Psilocybe
Includes Psilocybe s.s. taxa from this study
Tab2: Non-Psilocybe
Taxa found to not be Psilocybe s.s. from this study
Supplementary Table 3: RBB gene numbers, contigs, clustering results, and RBB method comparison to Exonerate
Gene and cluster recovery comparison of Reciprocal Best Blast and Exonerate methodology.
Tab1: Augustus gene prediction
Results for Psi cluster gene prediction using Augustus and RBB (reverse best blast) approach.
Tab2: Exonerate protein alignment
Results for Psi cluster gene prediction using Exonerates protein2genome function
Tab3: Augustus-Exonerate comparison
Comparison of Augustus and Exonerate output for gene prediction and contig placement.
Supplementary Table 4: Toplogy constraint testing: Individual model results
Individual model results model results and +/- symbols to indicate significance.
=====Supplementary_Information_and_Figures.zip=====
====Figures_full_resolution.zip====
High resolution copies of Figures 1-3 in both PDF and PNG format.
PDF file including all supplementary results and discussion along with supplementary table and figue legends.
PDF file Including all supplementary figures.
=====MSA_stats.zip=====
Multiple sequece alignment statistics generatned for the Psilocybe only data set used for Summary coalescent and concatened phylogenetic analysis. Stats files were generated using AMAS.py (see methods for paramaters).
=====PsiD_topology_test.zip=====
Toplogy constraint testing for HGT in Panaeolus and Pholiotina(see methods for paramaters).
==Constrained_tree==
Full IQtree directory output for PsiD Constrained tree analysis
==Unconstrained_tree==
Full IQtree directory output for PsiD unconstrained tree analysis
==Combined==
Full IQtree directory output for combined PsiD unconstrained toplogy constraint testing analysis
Funding
National Science Foundation, Award: 2114785, DEB