Flower bud development and differentiation in Opisthopappus: integrated morphological and transcriptional insights

Opisthopappus taihangensis and Opisthopappus longilobus are ecologically and horticulturally significant wild resources within the Asteraceae, yet the molecular mechanisms governing their flower bud differentiation remain poorly understood. Here, we integrated paraffin sectioning with RNA-seq to systematically characterize flower bud development and differentiation in both species. Over an approximately eight-week observation period, flower bud development was classified into nine distinct stages. Notably, O. longilobus completed differentiation approximately six days earlier than O. taihangensis , with nutrient accumulation predominantly occurring during the late stages. Weighted gene co-expression network analysis (WGCNA) identified four key modules, MEmidnightblue and MEcyan in O. taihangensis , and MEgreen and MElightcyan in O. longilobus , associated with flower bud differentiation. Forty-four common differentially expressed genes (DEGs) across these modules were enriched in six KEGG pathways, converging on four co-expression candidate genes ( VCP , PIPOX , PEX5 , and HSPA1_6_8 ) that were potentially associated with the activity of floral genes. Across all nine stages, inter-species DEGs primarily regulated protein synthesis and content, thereby influencing nutrient accumulation and distribution. Although both species shared conserved pathway frameworks, distinct gene sets were expressed within the same pathways in O. taihangensis and O. longilobus. Four circadian rhythm-related genes ( COP1 , ELF3 , LHY , and CDF1 ) were exclusively enriched in O. taihangensis , suggesting a potential association between species-specific circadian rhythm gene expression and the relatively prolonged flower bud development of O. longilobus. Collectively, these findings provide a comprehensive atlas of gene expression dynamics during flower bud differentiation in Opisthopappus , laying a foundation for dissecting the molecular regulation of flowering time and advancing our understanding of flower bud development in cliff-dwelling plants.