Haplotype-phased genome revealed the butylphthalide biosynthesis and hybrid origin ofLigusticum chuanxiong

Abstract

AbstractButylphthalide, one type of phthalides, is one of the first-line drugs for ischemic stroke therapy, while no enzyme involved in its biosynthesis pathway has been reported. Here, we present the first haplotype-resolved genome ofLigusticum chuanxiongHort., a long-cultivated and phthalide-rich medicinal plant in Apiaceae. Based on comprehensive candidate gene screening, four Fe (II)- and 2-oxoglutarate-dependent dioxygenases (2OGDs) and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturase (P4,5Ds) that converts senkyunolide A to l-n-butylphthalide (l-NBP) and ligustilide to butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity inL. chuanxiong. Notably, comparative genomic evidence supportedL. chuanxiongas a diploid hybrid withL. sinenseas a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago (Ma). Our study is an icebreaker for the dissection of phthalide biosynthesis pathway and reveals the hybrid origin ofL. chuanxiong. These findings will facilitate the future metabolic engineering for l-NBP production and breeding efforts forL. chuanxiong.