A draft reference assembly of the Psilocybe cubensis genome

CONCLUSION

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?