Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae)

Abstract

Saposhnikovia divaricata, 2n = 2x = 16, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia and other diseases. Here, we assembled a 2.07 Gb and N50 scaffold length of 227.67 Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42948, and 42456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.

Complete biosynthetic pathway of furochromones and its evolutionary mechanism in Apiaceae plants

“…Based on 28.65 Gb PacBio CCS long reads, we assembled the genome to 1.95 Gb (Supplementary Table 1), which was consistent with the estimate by flow cytometry (1.74 ± 0.07 Gb) (Supplementary Fig. 7) and the published assembly 27 . The assembly contig N50 was 2.22 Mb and the Benchmarking Universal Single-Copy Ortholog (BUSCO) score was 96.1%, indicating good genome continuity and completeness (Supplementary Tables 2-3).…”