Gene copy number is associated with phytochemistry in Cannabis sativa

Gene copy number variation is known to be important in nearly every
species where it has been examined. Alterations in gene copy number may
provide a fast way of acquiring diversity, allowing rapid adaptation under
strong selective pressures, and may also be a key component of standing
genetic variation within species. Cannabis sativa plants produce a
distinguishing set of secondary metabolites, the cannabinoids, many of
which have medicinal utility. Two major cannabinoids -THCA and CBDA - are
products of a three-step biochemical pathway. Using whole genome shotgun
sequence data for 69 Cannabis cultivars from diverse lineages within the
species, we found that genes encoding the synthases in this pathway vary
in copy number. Transcriptome sequence data shows that the cannabinoid
paralogs are differentially expressed among lineages within the species.
We also found that copy number partially explains variation in cannabinoid
content levels among Cannabis plants. Our results demonstrate that
biosynthetic genes found at multiple points in the pathway could be useful
for breeding purposes, and suggest that natural and artificial selection
have shaped copy number variation. Truncations in specific paralogs are
associated with lack of production of particular cannabinoids, showing how
phytochemical diversity can evolve through a complex combination of
processes.