A chromosome-level Pinellia ternata genome assembly provides insight into the evolutionary origin of ephedrine and acrid raphide formation

The tuber of Pinellia ternata is broadly used in traditional herbal medicines in Asian countries. Here, we report a chromosome-level genome sequence of P. ternata. The genome of diploid P. ternata was 2.08 Gb and assembled into 13 pseudo-chromosomes containing 34,342 genes. P. pedatisecta is the closest-related species with a full genome sequence, and their divergence began approximately 11.55 million years ago. Comparative transcriptome analysis on various tissues suggested the enrichment of genes involved in phenylpropanoid biosynthesis and starch and sucrose metabolism in P. ternata tuber. The candidate genes of ephedrine biosynthesis in the phenylpropanoid pathway were identified. At least one gene for each synthase of ephedrine biosynthesis was predominantly expressed in the tuber. Notably, all four phenylalanine ammonia lyase genes were predominately expressed in tuber tissue. A series of genes involved in oxalate metabolism were found to be highly expressed in tubers, contributing to the high accumulation of oxalate in tubers as well as the formation of acrid raphide via reaction with calcium ions. There are 14 lectin genes in the P. ternata genome, which were all highly expressed in the tuber, explaining the acrid raphide formation. These findings provide new insight into ephedrine biosynthesis and acrid raphide formation.