Integrative Analysis of the Metabolome and Transcriptome Reveals Seed Germination Mechanism in Helleborus thibetanus

Helleborus thibetanus, an endemic species in China, is a medicinal and ornamental plant. The seeds exhibit epicotyl morphophysiological dormancy. In this study, we performed transcriptome and metabolome analyses at four stages: freshly harvested mature seeds (S1), radicle-emerged seeds (S2), seeds with 2 cm root length (S3), and plumule-germinated seeds (S4). A total of 70,383 unigenes were obtained. Furthermore, 768 and 686 metabolites were identified by positive ion mode and negative ion mode, respectively. The expression levels of genes involved in terpenoid backbone biosynthesis and downstream gibberellin (GA) biosynthesis pathways were higher in the S2, S3, and S4 stages, which suggests that GA was associated with seed germination. The expression level of embryo development genes was higher in the S1 or S2 stages. The genes related to cell wall metabolism (EXP, XTH/XETs) were highly expressed in the S2, S3, and S4 stages, which promoted cell wall loosening and endosperm weakening, thereby facilitating seed germination. The genes involved in sucrose and starch metabolism were highly expressed during embryo development and germination (S2–S4), which indicates that they provided essential nutrients and energy for H. thibetanus seed germination. Our results provide a foundation for further research and facilitate the propagation of H. thibetanus seeds.