Multi-omics profiling of Nanhaia speciosa and Nanhaia fordii: insights into lectin dynamics, nodulation, and triterpenoid saponin biosynthesis

Abstract

Background: Nanhaia speciosa (N. speciosa) has long been served as a traditional medicinal and edible plant. N. speciosa and Nanhaia fordii (N. fordii) are the only two species under the Nanhaia genus, but the latter is of limited use. As a closely related species, N. fordii has a highly similar appearance and taste to N. speciosa and was used in the market to impersonate N. speciosa with potential harm to health.

Results: To analyze the differences and underlying basis between N. speciosa and N. fordii, we conducted a comprehensive comparison of their genomic, transcriptomic, and metabolomic data. Using PacBio HiFi and Hi-C data, we achieved high-quality haploid genomes for both N. speciosa and N. fordii. Comparative analysis reveals the elevated expression of Wisteria lectin-like genes in N. fordii, corresponding with higher heat-resistance lectin content in N. fordii than in N. speciosa, potentially causing food poisoning due to increased lectin levels in the plant. Metabolomic analysis indicates that licorice saponins are the main components contributing to the sweetness in N. fordii and N. speciosa, making it the only reported plant, apart from the licorice genus, containing licorice saponins. Moreover, the nodulation key gene RPG cannot be expressed in the roots of N. speciosa, possibly explaining the ability of N. fordii to form nodules while N. speciosa cannot.

Conclusions: Leveraging high-quality haploid genome assembly and multi-omics analysis, our data provides a crucial foundation for identifying key metabolic components and candidate genes associated with important traits and for breeding new varieties of N. fordii and N. speciosa.

Keywords: Nanhaia fordii; Nanhaia speciosa; Chromosome-level genome; Isoflavonoids; Lectin; Licorice saponins; Nodulation.