Background
Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored.

Results
We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp.

Conclusions
The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

If Genome Biology had been launched today, instead of 11 years ago, it might well have been given the alternative title of "Transcriptome Biology".

While Genome Biology captured the millennial zeitgeist of genomics brought about by the project(s) to sequence the human genome, the breathtaking progress of this field in the intervening decade has brought us to a new frontier: the transcriptome.

The development of RNA-seq, which applies high-throughput next-generation sequencing technology to cDNA generated from RNA samples, has resulted in an explosion of transcriptome sequences. Not only does RNA-seq benefit from higher sensitivity than microarrays, it also does not require the a priori knowledge needed for constructing chips; this flexibility has infused the transcriptome explosion with a biologically diverse character and encompassed many species not well covered by commercially available microarrays.

Species such as Cannabis sativa, a plant with a 'split personality', whose Dr Jekyll, hemp, is an innocent source of textiles, but whose Mr Hyde,