De novo assembly and transcriptome analysis of Hylocereus undulatus during development

High-throughput sequencing was used to analyze the gene expression of the reproductive buds, fruits, and shoots of Hylocereus undulatus Britt ‘Dahong2’ at different developmental stages. In total, 468.68 Gb of raw data were generated and de novo assembled into 239 152 transcripts and 162 519 unigenes. Approximately 53.74% of all unigenes were annotated based on seven public databases. In total, 600 283 SNPs and 56147 SSRs were identified from 43 506 and 16 251 unigenes, respectively. Gene expression analysis showed that 31, 7, 5, 152, 17, 63, 17, and 8 unigenes were specifically expressed in Fl510, Fl513, Fl514, Fl518, F711, F715, S513, and S419, respectively. Through GO and KEGG enrichment analyses, several unique GO terms and metabolic pathways in different tissues were identified; for example, terpenoid backbone biosynthesis (ko00900) showed significant enrichment in Fl510. We also focused on the molecular mechanism of H.undulatus ‘Dahong2’ flower development and identified a suite of unigenes involved in floral development, including COL, FT-like, meristem identity, and organ identity genes.