Integrated transcriptome sequencing approach provides insights into the mechanism of stamen petaloidy in Clivia miniata

Abstract Background Clivia miniata Regel, belonging to the Amaryllidaceae family, is a high valuable ornamental plant, and its double-flowered cultivars has a higher ornamental and economic significance. The formation of double flowers in C. miniata is primarily driven by stamen petaloidy, but the underlying molecular mechanisms remain poorly understood. Transcriptome sequencing has become a powerful approach for elucidating the molecular pathways underlying floral development. However, the transcriptomic mechanisms governing stamen petaloidy remain almost unexplored in C. miniata . Results Comparative transcriptome sequencing of buds and tepals from single-, semi-double-, and double-flowered C. miniata morphotypes yielded 127,524 assembled unigenes (average length 961 bp), with 38.38% annotated in public databases. Significant transcriptional reprogramming during stamen petaloidy was identified, including 44,140 and 40,278 differentially expressed genes (DEGs) in bud and tepal comparisons, respectively. These DEGs were significantly enriched in metabolic pathways and plant hormone signal transduction (particularly auxin signaling), with 209 hormone-related DEGs involving auxin, gibberellin, cytokinin, and jasmonic acid pathways. Numerous transcription factors, including members of the MYB, WRKY, bHLH, NAC, and bZIP families, as well as MIKC-type MADS-box genes (e.g., B-class CmPI_1 ), exhibited marked changes in expression. Weighted gene co-expression network analysis (WGCNA) further identified a core module associated with stamen petaloidy. Quantitative real-time PCR (qRT-PCR) analysis confirmed 13 key genes—including CmPI_1 , several transcription factors, and the jasmonic acid signaling gene CmJAR1L —showing significant upregulation, with expression levels positively correlated with the degree of petaloidy. Conclusions This study provides a comprehensive characterization of the transcriptomic features underlying stamen petaloidy in C. miniata . The identification of a core regulatory module involving hormone signaling, transcription factors, and floral identity genes offers key insights into the mechanisms of double-flower formation in monocotyledonous plants. These results establish a foundation for marker-assisted breeding and genetic improvement of floral traits in clivia and related ornamental monocotyledons.