Thursday, May 26, 2016

Brave New World

Fig.1. Cannabis sativa. (Credit: Biodiversity Heritage Library)

In a laboratory, just outside downtown Portland, Mowgli Holmes and his team at Phylos Bioscience are embarking on a brave new world.

“We’re creating the first genetically defined collection that has ever been,” he said. “... We know less about it than any other crop.”

That crop Holmes is referring to is cannabis, and that collection he and his team of genetic researchers have been working on the past couple of years is an extensive genomic dataset. Holmes and his group will expand upon the "draft" genomics work previously done.

“We basically needed to bring modern science and consistency to the industry,” said Holmes, chief scientific officer at Phylos Bioscience.

Legal loopholes in the name of genomics

Although Holmes works with herbaria and academic collections with cannabis specimens, there are certain restrictions to his research without a Drug Enforcement Administration research license. Cannabis samples can’t be transported across state lines, even for research purposes, so Holmes has set up a network of partner labs. Researchers extract the DNA from samples and ship the DNA to Phylos Bioscience to begin genomic testing.

“And we’ve had to develop all these tools to help individuals send us legal samples that don’t have anything illegal in it, but do have DNA in them,” Holmes said. “So that’s all been interesting and complicated.”

Holmes says they’ve figured out a whole variety of ways to legally ship genetic samples, from extracting pure DNA, to using DNA-stabilizing filter paper that plant tissue can be rubbed on, to shipping non-viable seeds. As long as the sample doesn’t contain illegal plant material or Tetrahydrocannabinol (THC) itself, then shipping is legal.

“We’re getting the hang of it now, but it definitely took a while to figure out how to do,” Holmes said.

Once DNA samples arrive at the Plylos Bioscience lab, Holmes said the samples will be processed as normal DNA lab.

“You have to care about the plant a lot to care about the information,” he said. “But we’re really just duplicating what people have done for human genetics.”

Cannabis’ future

“The way modern agriculture works these days is there’s quite a lot of genetic information,” Holmes said. “So we have really deep genomic resources for all the major crops, and they really drive the creation of new plant varieties.”

Genomic identity will assist in agricultural breeding programs, plant sex tests and strain identification tests. And while driving agricultural programs is important in the research he and his team are conducting, Holmes said cannabis is more than a crop.

“The funny thing about cannabis is it’s an agricultural crop, but it’s also a vice; it’s also a source of medicine,” he said. “And so most agriculture, you just think about food, but this agriculture that’s going to produce a complete pharmaceutical pipeline. It’s going to have cultural impacts. On the hemp side it’s going to produce oil, seed, fiber.”

Fig.2. Phylos Bioscience's Galaxy interface.

In terms of Phylos Bioscience’s future, on April 20, the group launched The Galaxy, a 3-D map of the relationships between cannabis varieties. Working alongside Rob Desalle, a curator and phylogeneticist at the American Museum of Natural History, Holmes and his team have animated what connections between the 1,500 varieties of ancient and modern samples look like. Users of The Phylos Galaxy can click through glowing dots on the screen to find relations organically or they can choose “Journey” mode to take them through the 3-D landscape.

“It’s just a plant that does tons of things. So when you’re breeding new varieties, you have lots of goals besides yields or flavor,” Holmes said.


A plant used in the production of industrial hemp fiber or a psychotropic drug or medicine.
Most commonly known as THC, it’s the main psychoactive element in cannabis varieties.


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