A chromosome level reference genome of Diviner's sage (Salvia divinorum) provides insight into salvinorin A biosynthesis.

Diviner's sage (Salvia divinorum) produces salvinorin A (SalA), a hallucinogen that activates the human κ-opioid receptor and may help treat chronic pain, addiction, and PTSD. Only two of the roughly twelve steps in SalA's biosynthesis were known. A high-quality chromosome-level genome assembly was produced, with an N50 of 41.4 Mb and 98.4% BUSCO completeness. The diploid genome is about 541 Mb. Two diterpene biosynthetic gene clusters were found, rich in new cytochrome P450s and crotonolide G synthase, which forms an early dihydrofuran ring. Other enzyme classes for later steps were scattered across the genome. Most candidate genes were not induced by methyl jasmonate. This genome enables discovery of the remaining SalA pathway steps.

Study at a glance

Abstract

Diviner's sage (Salvia divinorum; Lamiaceae) is the source of the powerful hallucinogen salvinorin A (SalA). This neoclerodane diterpenoid is an agonist of the human Κ-opioid receptor with potential medical applications in the treatment of chronic pain, addiction, and post-traumatic stress disorder. Only two steps of the approximately twelve step biosynthetic sequence leading to SalA have been resolved to date. To facilitate pathway elucidation in this ethnomedicinal plant species, here we report a chromosome level genome assembly. A high-quality genome sequence was assembled with an N50 value of 41.4 Mb and a BUSCO completeness score of 98.4%. The diploid (2n = 22) genome of ~ 541 Mb is comparable in size and ploidy to most other members of this genus. Two diterpene biosynthetic gene clusters were identified and are highly enriched in previously unidentified cytochrome P450s as well as crotonolide G synthase, which forms the dihydrofuran ring early in the SalA pathway. Coding sequences for other enzyme classes with likely involvement in downstream steps of the SalA pathway (BAHD acyl transferases, alcohol dehydrogenases, and O-methyl transferases) were scattered throughout the genome with no clear indication of clustering. Differential gene expression analysis suggests that most of these genes are not inducible by methyl jasmonate treatment. This genome sequence and associated gene annotation are among the highest resolution in Salvia, a genus well known for the medicinal properties of its members. Here we have identified the cohort of genes responsible for the remaining steps in the SalA pathway. This genome sequence and associated candidate genes will facilitate the elucidation of SalA biosynthesis and enable an exploration of its full clinical potential.