The chromosome‐level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis

Abstract

SUMMARY Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome‐scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi‐C sequencing technologies. The genome was predicted to contain 43 202 protein‐coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole‐genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.

Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong

“…S6 to S8). Consistent with the previous studies ( 37 ), we only detected one whole-genome duplication (WGD) event shared by the subfamily Apioideae and did not observe any recent specific WGD event for L. chuanxiong (figs. S6 and S9).…”

Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid–flavonoid pathway in Thymus mongolicus

“…This genomic evolutionary feature is particularly evident in the study of medicinal plants. For instance, in the genome of Angelica sinensis , genes involved in the biosynthesis of furanocoumarins have independently evolved in the families Moraceae, Fabaceae, Rutaceae, and Apiaceae after the ζ and ε WGD [ 110 ]. Arctium lappa retains specific genes that involved in cellulose metabolism, which may play an important role in the formation of cell walls in this plant [ 111 ].…”

Comparative-genomic analysis reveals dynamic NLR gene loss and gain across Apiaceae species

“…Apiaceae species have always played an important role in socio-economic and human life, among which Angelica sinensis, Bupleurum chinense, Centella asiatica and O. javanica are medicinal plants (Lu and Li, 2019;Sun et al, 2020;Liu et al, 2022), as well as Apium graveolens, Coriandrum sativum and D. carota are vegetables (Fox et al, 2022). Previous studies have shown that the Ks peak of the paralogous genes in five Apioideae species, including Daucus carota, Oenanthe javanica, A. sinensis, C. sativum and A. graveolens, corresponded to a recent WGD (whole genome duplication) event, possibly specific in Apioideae instead of Mackinlayoideae (Han et al, 2022). A variety of pathogens are known to be capable of infecting Apiaceae plants and causing economic losses (Fox et al, 2022).…”