Pitaya is an important economic fruit worldwide due to its numerous health benefits. The systematic understanding of the mechanism underlying flower development is essential to obtain higher fruit yield and quality. However, the genetic mechanism of flower development is not yet investigated in pitaya. Herein, a transcriptome analysis was performed to determine the transcriptional changes during flower development in red-flesh pitaya by utilizing nine different stages of flower development.

A total of 95412 unigenes was generated with a mean length of 913 nt, and N50 value of 1878 nt. Comparative transcriptomic analysis showed many differentially expressed genes (DEGs) among the flower growth stages. Furthermore, an array of key DEGs were enriched in hormone signaling, transcription, carbohydrate transport, and energy production pathways. In particular, indole-3-acetic acid, abscisic acid, ethylene-responsive transcription factor, constans-like, teosinte branched 1/cycloidea/proliferating cell nuclear antigen factor, apetala1-like, agamous-like MADS-box protein, sepallata, growth-regulating factor, putative axial regulator yabby, leafy/floricaula homolog, and MYB gene-associated transcription factors displayed altered expression, suggesting their critical roles in floral organ development of pitaya. Besides, genes related to sugar synthesis, transportation, and utilization mediate flower growth regulation in pitaya. Eleven genes were selected to perform qRT-PCR analysis to verify the results of the RNA sequencing.