Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy

The opium poppy has been a double-edged sword for the development of human civilization: the products of its pharmaceutical alkaloid pathways provide incalculable benefits for pain relief, addiction treatment, and a potential anti-cancer drug, while also driving historic and current epidemics in opioid addiction and overdose deaths. As a product of natural variation and artificial selection within the species, different lineages exhibit striking variation in their alkaloid profiles. Some varieties contain high levels of morphine and codeine, whereas others accumulate copious quantities of thebaine and oripavine at the expense of morphine and codeine. As the genome provides the key to understand the basis for this variation, we assembled a chromosome-scale draft genome of the opium poppy and sequenced 10 varieties with different alkaloid profiles.