show Abstracthide AbstractWe performed a comparative comprehensive analysis of the transcriptome dynamics of two cultivars with obvious difference in the number of carpels ('Fenmiantaosai' and 'Jingshunfen') in Paeonia rockii by combining the next-generation and single-molecule long-read RNA-seq techniques. We present high-quality sequencing products. Our results summarize a valuable collective of gene expression profiles, and provid a precious resource that reveals the molucular mechanism of regulating the carpel development in tree peonies and other woody flower crops.