Using high-fidelity single-molecule sequencing, the authors produced a 46.6 Mb draft genome assembly of Psilocybe cubensis in 32 contigs (46% GC, N50 3.3 Mb) with 97.6% BUSCO completeness. The psilocybin biosynthesis cluster resides on a single 3.2 Mb contig and the dataset is available from NCBI BioProject PRJNA687911 and PRJNA700437.
We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is available from NCBI BioProject with accessions PRJNA687911 and PRJNA700437 .
C-S. and colleagues report that they generated a highly contiguous draft genome assembly for Psilocybe cubensis. They state the assembly markedly improves contiguity relative to the existing reference at JGI (the N50 contig lengths are described as about 75-fold greater) and argue that this reference will facilitate identification of genetic variation affecting the biosynthesis of tryptamine-derived compounds such as psilocybin, psilocin, norpsilocin, baeocystin, norbaeocystin and aeruginascin. Peer commentary embedded in the extracted Conclusion praises the use of high‑accuracy long‑read sequencing and an advanced bioinformatics pipeline, and notes that the authors have made data openly available to enable replication. The commentators raise a potential caveat that the assembly might represent a composite (metagenome‑like) result rather than a single homogeneous haploid genome, because fungi can have multiple nuclei per cell with different haplotypes. This possibility is offered as an alternative explanation for a reported large insertion in the norbaeocystin methyltransferase (psiM) locus. The commentators recommend additional contextual data to address such concerns, in particular more background on the Psilocybe cubensis ‘‘Penis Envy’’ (PE) strain used (its origin and clonal propagation history). They suggest alternative genetic hypotheses for PE’s reported higher potency — for example, a mutation in psiK affecting drug/prodrug ratios rather than the psiM insertion — and note that polymorphisms in other biosynthetic or SAM salvage pathway genes could interact with the insertion. As practical follow‑ups they propose genotyping multiple strains for the reported ~4.6 kb insertion and associated single nucleotide polymorphisms to clarify the mechanism, and expanding comparative analyses to include genomes such as P. serbica var. bohemica provided chemotypic data are available. The Conclusion as extracted ends by noting the study’s aim to provide a high‑quality reference for the species and posing a question about the appropriateness and technical soundness of the protocols employed.
Papers cited by this study that are also in Blossom
Fricke, J., Lenz, C., Wick, J. et al. · Chemistry A European Journal (2018)
A highly contiguous Psilocybe cubensis genome has been generated. The N50 contigs lengths are 75 fold more contiguous than the existing assembly available at JGI. This reference can aid in the identification of genetic variation that may impact psilocybin, psilocin, norpsilocin, baeocystin, norbaeocystin and aeruginascin production. 1 Egret Bioscience Ltd., West Kelowna, Canada 2 Lighthouse Genomics Inc., BC, Canada McKernan and colleagues present on the first highly contiguous draft genome for the magic mushroom Psilocybe cubensis. We commend their use of High accuracy long read sequencing and an advanced bioinformatics pipeline to build a much more complete picture of the P. cubensis genome and for making it openly available to the public with the promise the genetic architecture of tryptamine expression in magic mushrooms. The methods employed are state of the art and the authors provide sufficient access to the data to enable peers and the public to replicate the experiment. While they acknowledge that the HiFi sequencing approach comes with great advantages, in particular greatly improved contiguity and and BUSCO completeness scores compared to other P. cubensis genomes published to date, the authors did not acknowledge that fungi can have multiple nuclei in a cell, sometimes with completely different haplotypes. As such, we posit that their assembly could possibly be a metagenome assembly, rather than the assembly of a single genome, thus providing an alternative explanation to the large insertion detected in the norbaeocystin methyltranferase (psiM) gene. Perhaps a means to provide a remedy to this is to provide some additional background on the P. cubensis Penis Envy (PE) strain, in particular the alleged origin of the PE mutant and its probable clonal propagation. While anecdotal at best, the fabled "mutation" of PE appeared and was selected from a phenotype of an amazonian P. cubensis accession, as a towering fruiting body with a pale cap and missing partial veil, which was then preserved via clonal propagation. The mutant is also described as being more potent that most other P. cubensis strain, leading to the hypothesis that it had a skewed drug to prodrug ratio (psilocyn/psilocybin) which would hint to a mutation in the psiK gene as opposed to the large insertion in psiM. Other putative mechanisms could be polymorphisms at other loci involved in the psilocybin biosynthetic pathways as well as ancillary genes involved in the SAM salvage pathway (e.g. ref 1), a list of putative functional SNPs that may interact with the large insertion is shown here from an earlier version of the P.cubensis genome. Genotyping several strains at the 4.6kb insertion and ancillary SNPs may help shed light on the mechanism behind the higher perceived potency of PE compared to other P. cubensis strains and other species in the Psilocybe and Panaeolus genus, In that vein, the authors may gain additional insight by including the P. serbica var bohemica genome to their comparative analysis, provided that chemotypic information associated with each accessions is made available. The study was undertaken in order to provide a high quality reference genome for the species. To date, the genomes in the species and genus are fragmented more than is desirable for basic and applied comparative investigations of genome content and architecture. Are the protocols appropriate and is the work technically sound?
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