Comparison of gene expression in female cannabis flowers, and gene copy number, between marijuana (PK) and hemp ('Finola'). (a) A scatter plot of RNA-Seq read counts for all representative transcripts in marijuana and hemp, expressed as log2 RPKM. Specific subsets of transcripts are shown in color, as indicated in the key. The dashed line represents the relative enrichment of trichomes in the marijuana strain, inferred from the ratio in expression of trichome-specific genes, as defined in the text. Gene symbols/abbreviations: CAN - known and putative cannabinoid pathway genes; HEX - putative hexanoate pathway genes; GPP - GPP pathway genes; MEP - MEP pathway genes; TF - putative transcription factors according to PFAM, with at least a 4-fold change in expression in PK relative to 'Finola'; MYB - Myb-domain transcription factors previously suggested as trichome regulators. (b) A scatter plot of the log2 median read depth (MRD) of genomic DNA-Seq reads that aligned uniquely to the PK transcriptome. Genomic reads were trimmed to a length of 32 bases prior to alignment with Bowtie, to allow for mapping close to exon junctions. The lack of outliers in the scatter plot indicates that there have been relatively few changes in gene copy number between marijuana and hemp. (c) The relative RNA-Seq expression of individual genes in the cannabinoid pathway and precursor pathways (is shown on the left), adjusted for enrichment of trichome-specific genes (i.e. relative to the dashed line in panel a). The median genomic DNA read depth for the same genes is shown on the right. The box plots reflect the variation in the depth of coverage of uniquely aligned genomic DNA reads across each transcript, with the median coverage distribution across all transcripts shown as reference (All). Reads that are likely derived from pseudogenes are marked by the symbol [P]. While there is increased expression of most cannabinoid genes in the HEX and CAN pathways (left) in PK, this does not appear to be due to an increased representation of these genes in the PK genome relative to the 'Finola' genome (right).
van Bakel et al. Genome Biology 2011 12:R102 doi:10.1186/gb-2011-12-10-r102