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Background  Quantitative variation of floral organs in plants is caused by an extremely complex process of transcriptional regulation. Despite progress in model plants, the molecular mechanisms of quantitative variation remain unknown in woody flower plants. The  Paeonia rockii  originated in China is a precious woody plant with ornamental, medicinal and oil properties. There is a wide variation in the number of carpel in  P. rockii , but the molecular mechanism of the variation has rarely been studied. Then a comparative transcriptome was performed among two cultivars of  P. rockii  with different development patterns of carpel in this study.    Results  Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in  P. rockii . Then clustering pattern and weighted gene coexpression network analysis (WGCNA) indicated that 15 candidate genes were likely involved in the carpel quantitative variation, including floral organ development, transcriptional regulatory and enzyme-like factors. Moreover, transcription factors (TFs) from the MYB, WD, RING1 and LRR gene families suggested the important roles in the management of the upstream genes. Among them,  PsMYB114-like ,  PsMYB12  and  PsMYB61-like  from the MYB gene family were probably the main characters that regulated the carpel quantitative variation. Further, a hypothetical model for the regulation pattern of carpel quantitative variation was proposed in which the candidate genes function synergistically the quantitative variation process.    Conclusions  We present the high-quality sequencing products in  P. rockii . Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. The DEGs are candidate for functional analyses of genes regulating the carpel quantitative variation in tree peonies, which provide a precious resource that reveals the molecular mechanism of carpel quantitative variation in other woody flower crops.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-6036-z) contains supplementary material, which is available to authorized users.

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii