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.

Saposhnikovia divaricata is a high-demand medicinal plant containing various bioactive metabolites (e.g., chromone). However, root rot disease leads to a dramatic reduction in the yield and quality of S. divaricata. The use of rhizospheric microorganisms is one of the best strategies for biological control. In this study, a total of 104 fungi isolated from the rhizospheric soil of S. divaricata plants were examined for their different antifungal properties. Subsequently, strain MR-57 was selected as a potential stock for biocontrol due to its broad-spectrum antagonistic activity against pathogens, including F. equiseti. Based on the analysis of morphological properties and rDNA internal transcribed spacers (ITSs), strain MR-57 was identified as Acrophialophora jodhpurensis (GenBank No. OK287150.1), a newly recorded species for China. In an in vitro antifungal assay, the culture filtrate of strain MR-57 significantly reduced the conidial germination rate and induced alterations in the mycelia morphology of F. equiseti, such as deformation and degradation. To assess the antifungal efficacy of MR-57 against root rot disease and the properties promoting the growth of S. divaricata, pot experiments were performed under natural outdoor conditions. The results indicated that co-inoculation with MR-57 delayed the occurrence of S. divaricata root rot and showed a control efficacy of 65.41% (p < 0.05) based on the measurement of suppressed disease lesions. Additionally, MR-57 successfully colonized and formed a stable population in the soil in which S. divaricata was grown, and it exhibited a consistently positive effect on the promotion of the growth of S. divaricata plants. In short, Acr. jodhpurensis MR-57 could be considered for the development of a potential biocontrol agent for the management of S. divaricata root rot caused by F. equiseti.