SAN DIEGO (GenomeWeb) – At the Plant and Animal Genomes conference this week, Medicinal Genomics senior advisor Timothy Harkins shared early results from a new genome: a de novo cannabis genome assembly produced with funding from the cryptocurrency DASH.
The researchers plan to share their work in an open-source paper with an alternative peer review strategy that involves paying reviewers $1,000 a pop for their time, while making reviewer identities and reviews transparent.
The Boston-based firm used Pacific Biosciences' long-read sequencing technology, Phase Genomics Hi-C data, and other approaches to assemble a high-quality de novo genome assembly for the Jamaican Lion cannabis strain, a "type II" cannabis chemovar identified more than a decade ago that produces both cannabidiol (CBD) and tetrahydrocannabinol (THC) compounds.
In the company's proposal for DASH, available online, Medicinal Genomics argued that funding the project would offer its cryptocurrency partner an opportunity to "make DASH a household name in three different $20 billion industries" — genomics, scientific publishing, and the cannabis market.
The project secured initial funding from DASH last spring, and maintained DASH support until October.
After putting together an initial genome assembly in early August, just 60 days after funding kicked off, the team incorporated additional data, including reads produced with newer PacBio sequencing chemistry, for a 3.7 megabase Falcon Assembly that was ready for publication by late October.
It was a demanding timeline, according to Harkins, who called it a "rocket ship of a project." That rapidity in part reflected cryptocurrency-based funding for the effort, he explained. DASH renews its funding each month through a competitive process — a system that demands speedy results.
Challenging timeline aside, the cryptocurrency-based funding stream was appealing due to difficulties pursuing federal funding for research on a plant that is currently classified as a Schedule I drug by the US Drug Enforcement Agency, despite medical and/or recreational cannabis legalization in many states.
Harkins shared results from some preliminary analyses on the new genome at PAG, including a look at active and inactive versions of tetrahydrocannabinolic acid synthase genes, which belong to the THC pathway, and chloroplast sequence data pointing to chloroplast heteroplasmy in the plant.
The investigators have teamed up with New England Biolabs to profile methylation in flowers from three cannabis plants: a female parent, a female clone seeded by a male sibling, and a male — work that revealed a propensity for enhanced methylation in the female flower tissues.
The team also plans to analyze RNA sequence data in cannabis tissues, Harkins said, and will continue improving the genome assembly and characterizing cannabinoid production in Jamaican Lion, while searching variants that may inform future marker-assisted breeding efforts.
Meanwhile, Medicinal Genomics is publishing the Jamaican Lion genome on the blockchain with "crypto-incentivized, blockchain-recorded peer review" (CIBR). The CIBR approach is outlined in more detail in an article on the company's website, where the authors discussed issues with the existing peer-review process, and noted that "[f]ree work is always deprioritized over paid work."
"To address financial conflicts that arise from directly paying for review, we utilize censorship-resistant blockchains to record all communication between the authors and the reviews," they explained. "Reviewers must stake their reputation on the review and must declare no financial conflicts in the review process other than the cryptocurrency incentivization for the review."