Medicinal Genomics Publishes Genome of Psilocybe Cubensis

Scientists at Medicinal Genomics, a specialist cannabis testing and genetics screening firm, have published a peer-reviewed, highly-contiguous reference genome for the psychedelic mushroom species Psilocybe cubensis.

To learn more about the significance of this reference genome, the challenges that come with studying psychedelics, and the future of this field of study, Analytical Cannabis caught up with Kevin McKernan, founder and chief science officer of Medicinal Genomics.

Building a better reference genome

Just as the term cannabis can refer to one of several hundred unique cannabis strains, there are several individual magic mushroom species that are found in nature. These species, plus any off-shoot strains that may arise from genetic mutations, can contain different amounts of the tryptamine compounds psilocybin and psilocin that are responsible for the psychedelic high.

While there have been attempts to roughly quantify the amount of psychedelic compounds produced by different mushroom species, how these mushrooms produce these psychedelics is still not very well understood. By sequencing the genome of different psychedelic mushroom species, researchers hope that they will be able to find the answer.

“We know very preliminarily that all the ‘strains’ produce fairly different tryptamine profiles [...] which means we need to understand which strains produce which compounds,” Kevin McKernan told Analytical Cannabis. “And so this, this genotype-to-phenotype correlation is probably going to be as important in Psilocybe as it is in cannabis.”

“There are a few other references out there. We put one into NCBI a couple of years ago, and I think a group in Germany did as well, plus one or two other sites. But they were all done with an Illumina sequencing platform which leaves the genome fairly fragmented – it leaves it in pieces of about 50,000 base pairs.”

In such a fragmented state, there is a limit to how having these genomic data might be helpful. But by using newer analytical tools, it is now possible to create more contiguous reference genomes for wider applications. To create this latest reference genome, the Medicinal Genomics scientists used the HiFi sequencing platform from Pacific Biosciences, which was able to assemble the reads into 32 contigs of lengths up to 4.6 megabases.

“We have another manuscript in preparation that has put it into chromosomes,” McKernan said. “We used another technique from Phase Genomics called Hi-C, which is a chromatin capture system that organizes [the genome fragments] into chromosomes. We’ll be publishing that shortly, but in the end, it ends up in 13 chromosomes.”

The benefits of a highly contiguous reference genome

Having assembled the mushroom’s genome into such large parts, the Medicinal Genomics team hopes that this reference genome will enable more useful research into how these Psilocybe mushrooms produce their psychedelic metabolites. To that end, they are already turning attention to studying other psychedelic mushroom species.

“We have a second preprint on this right now that is currently under review, where we’ve sequenced 81 additional genomes in Psilocybe. Most of them are Psilocybe cubensis but there’s a few P. tampanensis, P. azurescens, P. galindoi as well,” said McKernan.

“The question is, do all of the Psilocybe species make psilocybin in the same way? Is it inherited amongst all of them, or have they each found different ways to make psilocybin? A really good standard reference genome helps you answer that question.”

“I hope that we will find some variants that are in these genes that might predict which of the strains make more psilocin versus psilocybin. Certain point mutations or deletions or copy number changes in those genes may push one particular strain for making a particular tryptamine profile versus another, and the genetics will help be able to help predict that.”

McKernan also believes that this reference genome, and others like it, could give rise to new genetic tools that may help legal cultivators of these mushrooms perform quality control checks.

“Just having genetic tools that can help segregate these things as to what percentage of the spores are in fact from Psilocybe versus what percentage of the background is bacteria or non-Psilocybe DNA, there will be some [quality control] QC tools people can use. I see it helping in the QC of the spores and making sure they are what people claim they are, and then also maybe being predictive of the expression of chemotypes,” McKernan said.

The future of psychedelics research

Many of the challenges facing psychedelics researchers today echo those experienced by cannabis researchers in the early days of state-level legalization. Restrictive prohibitions on cultivation and the transport of material between state lines means that psychedelic researchers are currently limited to just examining mushroom spores, as they contain no psilocybin and will not produce it unless they are germinated.

“All we can do is sequence spores for taxonomy purposes. We can’t do anything beyond that, which really limits what the science can do today. But you can still get a lot done by just understanding the diversity of what’s out there,” McKernan explained.

“What are the most popular spores being sold? How different are they between all the different spore providers? That’s something that we’ve addressed. How frequently are they contaminated with other bacteria? That’s something that we can also see from sequencing data. And then, of course, on the psilocybin synthesis pathways, what kind of sequence variation do we see across all the different species that are out there?”

“I should caveat all of this in that the species nomenclature we are using right now isn’t entirely verifiable,” he added, “We are just getting spores from spore banks and whatever they are labeled as is what we have to go with. We have no way of culturing these things to confirm or chemotyping them to confirm.”

While the exact names assigned to each of these mushroom spores are uncertain, this is a problem that more genetic testing could hope to solve; by collecting massive amounts of genomic data, it is possible to identify clusters of related strains and species. Medicinal Genomics’ Kannapedia is an example of this kind of genetics library for the cannabis industry, and McKernan says there are plans to house these Psilocybe data in a similar easy-to-use fashion.

McKernan is quick to emphasize that there are still questions and topics that are up for debate in this field, most pertinently, whether these unique mushroom species all produce psilocybin because of horizontal gene transfer or if it could be a case of convergent evolution. Now, as this field develops and more data can be filled into these discussions, piece by piece researchers are able to build up new roadmaps for understanding these psychedelic mushrooms.