Cannabis Phylotree

The cannabis phylogenetic tree or evolutionary tree shown below is a branching diagram or “tree” showing the inferred evolutional relationships among various cannabis strains—their phylogeny—based upon similarities and differences in their genetic characteristics. Here the genetic characteristics are the identity and frequency of Single Nucleotide Polymorphism (SNP) in the captured regions of each cannabis strain genome (see description in each Tab under the tree for details). Genetic distance is a summary measure of the genetic divergence between cannabis strains, and the genetic distance of any two strains is approximately proportional to the total length of the radial parts in the path connecting the two ”leafs”, which represent the two strains. SNPs of each strain are identified by DNA sequencing and bioinformatics analysis in our StrainSEEK™ Strain Identification and Registration Service.

strainSEEK V1: 850,000 bases are sequenced to 10X coverage in each plant. To generate reproducible amplicons randomly distributed across the genome, a restriction enzyme (NspI) is used to reproducibly digest the genome. A size selection of DNA is made with a SAGE Pipin Prep and sequenced on an Illumina sequencer (Reduced Representation Shotgun, Altshuler et al). 5,000 -10,000 SNPs per sample are usually obtained.

Hovering over a strain of interest will highlight the strain along with other strains whose genetic distances to the interested strain are color coded as following:

  • Red: Clones
  • Orange: Siblings
  • Yellow: Cousins
  • Green: Distant relationship
  • Blue: Breed with me for diversity

strainSEEK V2: 3.2 Million Bases are sequenced to 10X coverage in each plant using a targeted enrichment approach (SureSelect, Agilent). This targeted approach covers 34 genes in the cannabinoid and terpene synthase pathway while also covering thousands of randomly distributed SNPs from StrainSEEK V1, Sawler, Lynch and the Phylos Galaxy. As result, samples sequenced with this method can be cross compared to all data that is public as of 2017. This is 25X more sequence than other tests on the market and as a result is the most comprehensive sequencing tool for discerning clones from siblings and identifying uniqueness a given strain. The method delivers 25,000-50,000 SNPs across the genome with a concentrated contribution from chemotype related genes. The higher SNPs density enables Marker Assisted Selection.

This phylotree is derived using the intersecting high quality SNPs from StrainSEEK V1 and StrainSEEK V2. The SNPs with the higher information content in StrainSEEKV1 were carried over into StrainSEEK V2 for backwards compatibility during the upgrade.

Hovering over a strain of interest will highlight the strain along with other strains whose genetic distances to the interested strain are color coded as following:

  • Red: Clones
  • Orange: Siblings
  • Yellow: Cousins
  • Green: Distant relationship
  • Blue: Breed with me for diversity