Full-length transcriptome sequencing analysis and characterization of MADS-box genes in Rhododendron fortunei

Abstract Background Rhododendron fortunei, an endemic Chinese species, holds significant ornamental and economic value. MADS-box transcription factors play pivotal roles in regulating diverse aspects of plant growth and development. However, molecular biological research on R. fortunei remains limited, particularly concerning its MADS-box gene family. In this study, we present the first full-length transcriptome analysis of R. fortunei using SMRT sequencing technology, enabling identification and comprehensive characterization of its MADS-box genes. Results We obtained 40,782 high-quality unigenes, with an average length of 2,366 bp. In total, 39,214 (96.16%) unigenes were functionally annotated against seven public databases. Core biological functions of the unigenes were characterized through GO, KOG, and KEGG pathway analyses. A total of 956 LncRNAs and 2,051 TFs were further identified. Using the unigenes as reference, RNA-seq analysis delineated global gene expression patterns. Furthermore, we identified 36 MADS-box genes and characterized their physicochemical properties, phylogenetic relationships, and conserved motifs. Notably, 34 MIKC-type RfMADS genes exhibited tissue-specific expression across vegetative and floral organs, suggesting their functional relevance in R. fortunei floral development. Conclusions These findings advance our understanding of the genetic information of R. fortunei and establish a foundation for genetic studies. Moreover, this study paves the way for comprehensive exploration of molecular mechanisms underlying the MADS-box genes in floral development of R. fortunei.