Difference between revisions of "Cannabis sativa cultivar Chemdawg (marijuana)"

Revision as of 14:52, 23 August 2011

This genome was sequenced by Medicinal Genomics (located in the Netherlands). It was sequenced with one lane of the Illumina HiSeq (2x100) platform and assembled with CLCbio’s workbench. Additional information about the assembly and genome may be found: http://www.medicinalgenomics.com/the-c-sativa-genome/

You can access Cannabis in CoGe: http://genomevolution.org/CoGe/OrganismView.pl?oid=33804

Cannabis is a member of the plant order Rosales. Of sequenced genomes in that order, the peach genome is a fantastic comparator. The reason for this is due to its high-quality sequence and assembly and its genomic evolutionary history that does not contain any subsequent whole genome duplication event to the eudicot paleohexaploidy shared by nearly all dicots (at least the eurosids and the astrids). As such, its genome structure is probably very similar the common ancestor of order Rosales, and perhaps the eudicots as a whole. This likely ancestral state of its genome makes it quite suitable for generating a pseudoassembly of highly fractured, low quality genome assemblies such as this Cannabis genome. CoGe's tool SynMap has an algorithm to tile contigs along any other "reference" genome in CoGe.

The Syntenic path assembly of Cannabis to the peach genome may be viewed: http://genomevolution.org/wiki/index.php/Syntenic_path_assembly#Cannabis_sativa_.28marijuana.29_v._Prunus_persica_.28peach.29

This shows the Cannabis genome sequence contains nearly the entire gene content of Peach.

Syntenic path assembly and syntenic dotplots of the Cannabis sativa (marijuana) v. Prunus persica (peach)

SynMap has the ability to tile a contig level assembly against any other genome in CoGe using synteny. These pseudoassemblies can be printed out and then reloaded into CoGe. By having such high-order assemblies, as unreal and inaccurate as they are to the actual genome structure of an organism, permits using CoGe's other tools to rapidly compare genomic regions. This method can rapidly turn a 170,000 piece genome into something useful for comparative genomics.

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  Syntenic dotplot by [SynMap]. X-axis Cannabis sativa (marijuana); Y-axis Prunus persica (peach). Results may be regenerated: http://genomevolution.org/r/3wz3

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  Syntenic dotplot by [SynMap]. X-axis Cannabis sativa (marijuana); Y-axis Prunus persica (peach). The Cannabis genome was pseudoassembled against the peach genome using SynMap's Syntenic path assembly algorithm. The assembled genome was reloaded into CoGe and compared against the peach genome. Results may be regenerated: http://genomevolution.org/r/3x1o

GEvo analysis of pseudoassembly of Cannabis genome to peach

Note that the pseudoassembled contigs in Cannabis are identifiable by orange bars in the background of the Cannabis panel. These orange bars are the 100 Ns used to join neighboring contigs. Results may be regenerated at http://genomevolution.org/r/3x1u .