Chromosome-level genome assembly of <i>Salvia miltiorrhiza</i> with orange roots uncovers the role of Sm2OGD3 in catalyzing 15,16-dehydrogenation of tanshinones

Abstract

<i>Salvia miltiorrhiza</i> is well known for its clinical practice in treating heart and cardiovascular diseases. Its roots, used for traditional Chinese medicine materials, are usually brick-red due to accumulation of red pigments, such as tanshinone IIA and tanshinone I. Here we report a <i>S. miltiorrhiza</i> line (shh) with orange roots. Compared with the red roots of normal <i>S. miltiorrhiza</i> plants, the contents of tanshinones with a single bond at C-15,16 were increased, whereas those with a double bond at C-15,16 were significantly decreased in shh. We assembled a high-quality chromosome-level genome of shh. Phylogenomic analysis showed that the relationship between two <i>S. miltiorrhiza</i> lines with red roots was closer than the relationship with shh. It indicates that shh could not be the mutant of an extant <i>S. miltiorrhiza</i> line with red roots. Comparative genomic and transcriptomic analyses showed that a 1.0 kb DNA fragment was deleted in shh <i>Sm2OGD3m</i>. Complementation assay showed that overexpression of intact <i>Sm2OGD3</i> in shh hairy roots recovered furan D-ring tanshinone accumulation. Consistently, <i>in vitro</i> protein assay showed that Sm2OGD3 catalyzed the conversion of cyptotanshinone, 15,16-dihydrotanshinone I and 1,2,15,16-tetrahydrotanshinone I into tanshinone IIA, tanshinone I and 1,2-dihydrotanshinone I, respectively. Thus, Sm2OGD3 functions as tanshinone 15,16-dehydrogenase and is a key enzyme in tanshinone biosynthesis. The results provide novel insights into the metabolic network of medicinally important tanshinone compounds.