Why DNA Sequencing? 

Both Industrial Hemp and Cannabis can be bred to be more productive and more medicinal. Genomic information can be a helpful tool here. Sequencing of THC, CBD, CBC, and other genes in the cannabinoid and terpene synthesis pathways are be shown to be predictive of Cannabinoid expression and in our understanding of the medicinal components of the plant.

DNA Sequencing of the THC Synthase gene can provide valuable predictive medicinal information and better selective breeding information.  THC Synthase is a highly polymorphic gene. Up to 16 SNPs in 200bp implies wide genetic diversity in this gene.

 

The Cannabis Genome

The Cannabis Sativa genome has 10 autosomal chromosomes plus 2 sex chromosomes and mitochondrial and chloroplast genomes. The mitochondrial genome appears to be in 8 50Kilobase pair (kb)pieces which is substantially larger than human 16Kb mitochondrial genome.

Figure from Sakamoto et al.

 

Cannabis Sequence Similarity to other Species

Genome Sequence reveals high similarity to Ricinus Communis (Castor Oil), Carica Papaya (Papaya), Humulus Lupus (Hops) and Vitis Vinifera (Grape) Genomes.

BLAST Alignment of Cannabis Mitochondria contig has highest similarity to Ricinus communis

Chloroplast Genome from Cannabis is more similar to Morus Indica (Mulberry Bush)

Using the most advanced DNA sequencing tools, billions of DNA molecules can be sequenced in parallel for comprehensive genetic classification of Cannabis Strains. Medicinal Genomics has sequenced 65,000X more Cannabis DNA Sequence than exists in the public Databases in 2011.

Jim Knights assembly of the LA Confidential Mitochondrial and Chloroplast genomes assembled with 454 data.

medgen_chloro

medgen_mito

We have used HiSeq 2×100 sequencing for 131Gb of data on Chemdawg.

We also have access to 750bp 454 Sequencing for over 10Gb of Sequence on triple backcrossed, Cannabis Cup winner LA Confidential. A strain also well known for its use in extreme cases of Autism: http://uf4a.org/.

This sequencing technology has aided in phasing many CNVs in the genome governing chemotype.

454 offers the longest massively Parallel sequencing which enables phasing of highly polymorphic regions in CNVs of synthase genes which govern Chemotype

In addition, care has been taken to sequence Cannabis strains which have strict quality control and cloning efforts under way with DNA Genetics, NL.

Strains of interest Include:

  • Triple Backcrossed Pure Indica – LA Confidential.
  • Sativa, Hybrid- ChemDawg- Amsterdam
  • Recon- DNA Genetics cross with LA Confidential and Cannadential (offspring of female LA Confidential and Cannalope).
  • Chocolope- DNA Genetics

 

Massively Parallel short read sequencers like SOLiD and ILMN help to provide affordable high coverage of Cannabis genomes once there is a good reference genome.