The Magnitude of Medicinal Genomics’ Sequencing of 80+ Magic Mushroom Species

Written by Kevin McKernan

Interview Conducted by Jason S. Lupoi, Ph.D.

The appeal of magic mushrooms has, well, mushroomed over the past few years, as revived medical evidence points to their powerful healing potential for contemporary conditions like depression and post-traumatic stress disorder. Although these fungi have been alongside us for millennia, political plots have prevented us from recognizing their ultimate capabilities and ours.

But with the FDA branding psilocybin as a breakthrough drug for major depressive disorder, and Canada legalizing magic mushrooms for end-of-life care, scientists are taking advantage of newfound research pathways to unearth all they can. Medicinal Genomics, for example, has recently sequenced the genomes of over 80 mushroom varieties with the goal of better understanding how species in the Psilocybe genus are genetically comparable as well as how these mushrooms relate to lookalike species. [1]


Genetic Sequencing

So, what does it mean when the genome of a substance has been sequenced?

“Sequencing gives a catalog of the genes,” Kevin McKernan, chief scientific officer and founder of Medicinal Genomics explained. “If you sequence more than one species, you get a catalog of their genetic variation.”

The Psilocybe genus makes other molecules than psilocin and psilocybin, including baeocystin, norpsilocin, and norbaeocystin. “There’s an entourage of at least six compounds that are on people’s radar,” McKernan added.

Magic mushroom mycelium make beta-carbolines as well, including monoamine oxidase inhibitors (MAOI). MAOIs are a powerful class of antidepressants that treat depressive symptoms by preventing the degradation of molecules like serotonin, dopamine, and norepinephrine, all integral molecules for regulating mood. Beta-carbolines in magic mushrooms include harmine, harmaline, and tetrahydroharmine, all of which have different properties. McKernan says that one of these molecules may be psychoactive such that it may alter the way in which our bodies process these molecules. [2] “Some mushrooms make different levels of these compounds, so how do you breed mushrooms to maximize or diminish some of these molecules?” McKernan questioned. “We need to have the same type of genetic catalog as we do for cannabis.”

“There are 200 mushrooms that can make psilocybin but they are not all in the same species,” McKernan explained. “There are different genera, and therefore psilocybin-producing mushrooms are very diverse. So, we will need more than one P. cubensis genome and genomes from other species. We started off with sequencing the variety of P. cubensis known as Penis Envy.” McKernan says the key is to dissect the entourage effect to determine which genes are driving the effect.


Why Psilocybe?

I asked McKernan why Medicinal Genomics decided to sequence the genomes of Psilocybe species as opposed to doing something else?

“There were a couple of motivations,” McKernan answered. “On a personal level, my father was struggling with stage four cancer, and I was reading papers about the treatment of terminal cancer depression, which led me to the work that Johns Hopkins University is doing with psychedelics.

“I had sequenced one psychedelic mushroom species a while back to get a quick look, but I was nervous to publish the results. The market is maturing now, resembling how the cannabis industry began 15 or 20 years ago. Mushrooms may move through the regulatory process much quicker than cannabis, however, as there is a lot of sympathy for these compounds. Depression affects a lot of the population!”

One of the main rationales for sequencing psychedelic mushrooms regards the presence of imposter lookalikes. “Some of these psychedelic mushrooms grow wildly on the West coast,” McKernan reported, “but their lookalikes can be dangerous, so we need a polymerase chain reaction assay that can speciate them.”

One such lookalike is Galerina marginata also ominously known as the funeral bell or deadly skullcap. Ingestion of the mushroom toxins causes severe liver damage along with vomiting, diarrhea, hypothermia, and death if not treated immediately.

There’s also a rare, anecdotal phenomenon called wood lover’s paralysis, a temporary condition caused by ingestion of magic mushrooms that grow on wood. The phenomenon has been most associated with Psilocybe azurescensPsilocybe cyanescens, and Psilocybe subaeruginosa. The condition wears off as the mushrooms wear off, but it can be debilitating. “There’s something in the synthesis of these mushrooms that can cause the paralysis,” McKernan added. “Anesthesiologists are interested because very few compounds wear off this quickly. It might be a derivative of aeruginascin (a closely related compound to the frog skin toxin bufotenidine), an alkaloid found in the mushrooms.

“Right now, one of the challenges is to differentiate P. cubensis from wood lover’s species and Galerina marginata,” McKernan continued. “We can speciate a spore sample to see if it’s really P. cubensis, and if it has elements of wood lover’s or Galerina. This is important because we want to make sure that there are no regulatory concerns about products going to market, that there’s no reason to fear.”


Genetic Surprises

I asked Kevin if there were any surprises in the sequencing data that he did not expect to see?

“There were indeed,” he answered. “We had no idea about the level of variation. We surveyed four different spore providers. It is much easier to propagate clonally in mycology, and we found a consistency of spore providers if you just go off of the name.” This stands in contrast to variation in the genetics of cannabis varieties of the same name.

McKernan also noticed a sequencing artifact. “When you isolate DNA, it’s rare to get 100% of that organism. One thing that was really noticeable was that getting DNA from a spore is very hard. The spore makes hearty shells so the DNA can survive. If the spores are submerged in solution, you can get an enrichment of bacteria on the outside of the spore. For 20% of the samples, you can see another contaminant genome, so you need to peel apart the bacterial DNA from the fungal DNA in silico.”

There’s also variation inside the genes that make compounds like psilocybin and psilocin. For example, the PSIM gene leads to methylation, whereas the PSIK gene puts on a phosphate group, and the PSIH gene hydroxylates. “There were five or six genes that we paid close attention to that seem to be in the same neighborhood in the genome,” McKernan explained. “This gives us an understanding of the variation in the pathway.”



Medicinal Genomics has created the Psilocydia website that demonstrates the phylogenetic tree of the different mushroom species they have sequenced to date. McKernan says that one take home message is that many varieties with the same names cluster around each other.

“There is an occasional mis-identification. Some were not even in the genus, revealing how genetic analyses can be used to sort out occasional mix-ups. The tree helps to answer the question of how genetically related are these mushrooms? P. subaeruginosa is an Australian wood lover, and as such, it might make the same compound that causes the paralysis. This works also helps us to understand the geographic spread in the genetics.”


Knowledge Gaps

Psilocydia is described as “a technology platform that provides the foundation for research, selective breeding, safety testing, and innovation in the nascent psilocybin industry.” I asked Kevin what gaps currently exist that are paramount to fill for the psilocybin conversation to move forward?

“Chemotypes and mating types. If you plate the spores on a Petri dish, they won’t grow into each other unless there are specific pheromones present. The mycelium tangle with each other where they can swap nuclei.”

McKernan also pointed genes that control pigmentation such as the bag appeal of the albino line. These genes have been found in other mushrooms, but what genes cause this in Psilocybe?

Another aspect to understand regards large fruit growth. The WD40 gene accelerates the growth of the caps in other mushrooms. “When this gene is knocked out, the fungi don’t even fruit,” McKernan explained. “There could be genes that help us understand how to grow these things very quickly.”


Protecting Intellectual Property

Understanding the genetics can point to the art behind the science, which in turn, led us to discuss how a cultivator can protect their artistry. Medicinal Genomics has brought open access genetics via blockchain technology to the cannabis industry, and they are looking to do the same for magic mushrooms.

“It’s unclear how this will unfold in mycology, but in cannabis, you can’t trademark things that are illegal but you can patent,” McKernan explained. “Essentially, there are three different ways to protect your property in cannabis. A lot of growers are not in the matrix of bank accounts and patent lawyers, where it may cost $15,000 to file a patent, so they might just document what they have. They can’t get this notarized.

“Another option is to sequence the genome and put it on a distributed ledger that no one can change. You can take a hash of the genome as a signature, which is then distributed on millions of computers across the world that cannot be edited. If the signatures do become edited, they become “tamper evident”.

“Longer term, if a cultivator has a plant that’s worth protecting, they can talk to a patent attorney. The blockchain approach is the poor man’s approach which is akin to mailing it to yourself. This helps to neutralize the fear of people taking the data and running off with it because people can prove their data existed at an exact time with or without Medicinal Genomics.”


Inside the Crystal Ball

So, what does the future hold for magic mushrooms?

“At CANNMED, research was shared that involved mixing psilocybin and cannabis for breast cancer treatment. I’m particularly interested in how psilocybin may play a role in COVID 19. For example, selective serotonin reuptake inhibitors (SSRIs) such as fluvoxamine might be replaced by psilocybin. Psilocybin is very closely related to DMT which regulates the same sigma 1 receptor as Fluvoxamine’s proposed mechanism of action in C19. [3,4] I should point out that this is all very hypothetical, but psilocybin could provide an interesting bridge in playing a role in pandemic relief.”

Kevin pointed out an interesting intersection between cannabis and tryptamines. A 2022 paper demonstrated the presence of L-kynurenine and kynurenic acid in cannabis plants. [5] Therefore, cannabis may also play a role in the tryptamine pathway. “The physicians who know how to treat with cannabis might be the first to be open-minded to looking at mushrooms,” Kevin added. “There is low risk due to low toxicity. The whole medical realm of magic mushrooms is really exciting!”

McKernan also pointed to analytical tools as having the potential to accelerate the field in Psilocybe. “There are over 200 labs around the world that know how to operate with cannabis. These labs will likely be the first ones to be able to run mushroom analytics. The brainpower is primed and ready to explore this new market. For example, Steep Hill and SC Labs got their footing 15 years ago. If you had to bootstrap Psilocybe labs, it would slow everything down. The cannabis marketplace has the testing capacity, and cannabis cultivators would likely have an easy time growing these things. The two communities have a lot of synergy.”



[1] McKernan K, Kane LT, Crawford S, Chin CS, Trippe A, McLaughlin S. A draft reference assembly of the Psilocybe cubensis genome. F1000Res. 2021;10:281. [journal impact factor = 2.297; times cited = 0] [2] Blei F, Dörner S, Fricke J, et al. Simultaneous production of psilocybin and a cocktail of β-carboline monoamine oxidase inhibitors in “magic” mushrooms. Chemistry. 2020;26(3):729-734. [journal impact factor = 5.02; times cited = 20] [3] Fontanilla D, Johannessen M, Hajipour AR, Cozzi NV, Jackson MB, Ruoho AE. The hallucinogen N,N-dimethyltryptamine (DMT) is an endogenous sigma-1 receptor regulator. Science. 2009;323(5916):934-937. [journal impact factor = 47.728; times cited = 427] [4] Khani E, Entezari-Maleki T. Fluvoxamine and long COVID-19; a new role for sigma-1 receptor (S1R) agonists [published online ahead of print, 2022 Apr 6]. Mol Psychiatry. 2022;1. [journal impact factor = 13.44; times cited = 1] [5] Russo F, Tolomeo F, Vandelli MA, et al. Kynurenine and kynurenic acid: Two human neuromodulators found in Cannabis sativa L. J Pharm Biomed Anal. 2022;211:114636. [journal impact factor = 3.935; times cited = 0]

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Kevin McKernan

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