Video tip of the week: Highlights [heh] of the Cannabis browser

Yeah, I couldn’t resist. Stop groaning–lighten up! Ok, really, I’ll stop now. The Cannabis genome project is an interesting exploration of an important plant genome, with a bunch of new data, and you can examine all of it in their browser. They are using a custom version of the UCSC Genome Browser, which we know is a great way to visualize and query data that might be important to you. In this week’s tip we’ll see some of the data and how you can interact with it.

This browser provides access to two draft assemblies–one for a medicinal marijuana called Purple Kush, and one for a related hemp strain called Finola. Besides the reference scaffold assembly sequence data, they also deliver some transcriptome data sets that examine the expression data in various stages of plant tissues and development (stem, root, seeds, flower stages).

Also on the Purple Kush (PK) assembly they show the SNVs, or single nucleotide variants–sometimes called SNPs, that are different between the strains. They also have the variants for a hemp called USO-31. In the paper they also referred to variations in the medicinal Chemdawg strain that came out while they were working on their paper, and when I asked if they had plans to put those variants on the browser, they offered to do that for me! So now you can compare PK and Chemdawg with the two different tracks. Sweet! {thanks Harm and team!}

The SNPs/SNVs seem to be more important than copy number variations (CNVs) for the cannabionoid pathway genes, according to the authors. Plants often use multiple copies of genes of value to the plant as a way to increase expression of a gene. But when they looked at cannabinoid pathway genes they didn’t seem to have much of that, or at least not as much as they thought they might find. It looks like the small polymorphisms are making the difference among the strains probably affecting the expression levels. A nice handy feature of their browser is a table of the cannabinoid pathway genes (18 of 19 of them, according to the paper) on the Purple Kush landing page, with a diagram of the pathways. You can go directly to the locations of those genes in the scaffolds by clicking there. If there are multiple copies they are indicated separately. The pathway is also figure 3 in the paper, along with some analysis of the expression levels.

And the transcriptome data turned out to bring really crucial information on what was different between hemp and pot. Specifically, the data from the transcriptome analysis showed that the THCA synthase enzyme (THCAS on the browser) is actively and highly expressed in Purple Kush flowers, but it’s turned off in hemp. So you don’t get the tetrahydrocannabinol acid (THCA) product from the end of the pathway in hemp, you get cannabidioloc acid (CBDA) instead, which is not psychoactive.

Something else I learned: I did not realize that there were X and Y chromosomes in Cannabis. But now I know.

One of the strangest things I’ve ever encountered in a genome paper (and I read a lot of ‘em) was this:

The underlying mechanisms for this transcriptional control could probably be dissected using existing techniques, were there not severe legal restrictions in most jurisdictions on growing cannabis, even for research purposes.

Illegal to do much more of the necessary work. Hmm.  I think that’s a first in my genome reading. But it also complicates the analysis beyond this data. This is draft sequence, there’s more to learn–and elucidation of the pathways would help us to understand the medical properties quite a bit more. I guess we’re all safer for not knowing…or something….??? </end snark>

So you can check out all the current features on their local installation of the UCSC Genome Browser. They have the main tools you expect on a UCSC Browser, and the Table Browser, In-Silico PCR and BLAT for sequence searching. Although everything is green here instead of blue, the software functionality will be the same as on the main UCSC Browser. So if you want to learn how to use it, you can see our tutorials on the software features. They very kindly link to our training in their help documentation too.

Quick links:

CCBR Cannabis Genome Browser: http://genome.ccbr.utoronto.ca/

UCSC Genome Browser Introductory Tutorial, and links to the other UCSC tutorials as well: http://openhelix.com/ucsc

I also could not resist this screenshot:

Reference:

van Bakel, H., Stout, J., Cote, A., Tallon, C., Sharpe, A., Hughes, T., & Page, J. (2011). The draft genome and transcriptome of Cannabis sativa Genome Biology, 12 (10) DOI: 10.1186/gb-2011-12-10-r102

Also see some other good material on this work, from various sources:

Decoding Dope

U of S and U of T researchers team up to map the cannabis genome

Putting the high into high-throughput sequencing: the cannabis genome

How hemp got high