Sequencing Read QC

Complexity of the Cannabis Genome:

• 400Mb est via Next Gen Sequencing. Kew Gardens estimate of 700-800Mb
• Diploid
• 67% AT
• Highly Polymorphic (SNP every 10-20bp in Synthase genes)
• Highly repetitive
• Selective breeding for 30 years for chemotyptic QTLs
• 5-10 week breeding cycle
• Sativa, Indica, Ruderalis likely interbred

Due to this complexity we have incorporated a diverse set of tools to decode the Cannabis Genome.

• Breeding collaborations with DNA Genetics in Amsterdam to obtain triple backcrossed Pure Indica DNA from Cannabis Cup winner LA Confidential
• Roche has kindly provided early access to their 750bp run module on the GS-FLX+ platform. Over 15M 700bp reads (630 Average, 750 mode) of sequence was obtained through their service center. Preliminary assemblies are with CLC bio.
• 131 Gb of Illumina HiSeq 2 x 100 reads from 230bp inserts applied to a Sativa/Hybrid cultivar ChemDawg.
• Breeding collaboration with Greenhouse Seeds to advise on high CBD inbred landraces and Ruderalis DNA.
• We are investigating Long Mate Pair SOLiD sequencing for super contig generation and Ion Torrent for validation.
• 92Mb of RNA-Seq has become partially available this summer via a web portal blast server at Medicinal Plant Genomics Resource (unrelated and a different cultivars). http://medicinalplantgenomics.msu.edu/

Read Length from 454 750bp Run Module

•  Aug_01_2011
• Aug_02_2011
• Aug_4_2011