Medicinal Genomics sequences entire genomes of two therapeutic Cannabis strains

Aug 19 2011

Medicinal Genomics, a private company headquartered in Marblehead, Mass., USA and the Netherlands, announced today that it has sequenced the entire genomes of Cannabis sativa and Cannabis indica, representing two strains of the therapeutic plant. The genome assemblies, comprising over 131 billion bases of sequence, are the largest known gene collection of the Cannabis genomes and will be made publically available to the scientific community this fall. The genomic data is expected to aid in the advancement of research on the therapeutic benefits of the Cannabis plant for a wide range of health conditions, including cancer and inflammatory diseases.

"Despite compelling evidence of the therapeutic benefits of Cannabis, very little genomics research has been performed in this area," said Kevin McKernan, founder and head of scientific operations of Medicinal Genomics. "With the goal to sequence multiple Cannabis varieties, we initially took the approach of using short-read next generation sequencing technology on the C. sativa strain. We very quickly realized that this method was not going to provide a clear picture of the genome required to tease out the important biological pathways. This realization caused somewhat of a paradigm shift in the way we approached this project. At this point we moved to triple backcrossed cultivars and longer read technology."

Surprised in part by the finding that genomic variation between Cannabis strains is over 1%, a figure that is 10 times the variation of human genomes, the team at Medicinal Genomics turned to Roche's 454 Sequencing Center in Branford, Connecticut to sequence the Cannabis indica strain on Roche's new GS FLX+ System, the latest advance in long read next generation technology. The researchers obtained roughly 18x genome coverage with the 700-800 base pair long reads, enabling a high-quality draft assembly of this complex plant genome.

"I was stunned by the data quality and more impressively the read lengths of the data coming off the GS FLX+ Instruments," said McKernan. "With the long reads we can sort out the variation in the strain and phase alleles so that we can make biological sense of the sequencing data. We can assemble some key synthase genes into much longer phased blocks, allowing us to focus more on the biology and less on the computational concerns over collapsed polymorphic assemblies we were seeing with the shorter read systems."

"We are pleased to see an industry-renowned expert in the field of next generation sequencing recognize the value of the long reads offered with our new GS FLX+ System," said Todd Arnold, Vice President of Development at 454 Life Sciences, a Roche Company. "This project, along with other work on a variety of large plant and animal genomes, confirms the power of long reads for high-quality assembly and, most importantly, for correlating sequence content with biological significance."

Later this fall Medicinal Genomics plans to release the raw sequence data of the Cannabis indica genome as well as a full genome annotation. With the genomes in hand, researchers can begin to identify non-psychoactive compounds or enzyme pathways to better elucidate the therapeutic benefits of Cannabis, including the plant's anti-cancer properties. These pathways can be optimized in the plant or cloned into other hosts for more efficient biologic production. In addition, it may be possible through genome directed breeding to attenuate the psychoactive effects of Cannabis while enhancing the medicinal aspects.