Integrated high-throughput sequencing approach provides insights into the mechanism of flower development in pink-flowered strawberry

Pink-flowered strawberry possesses significant ornamental value; however, the molecular mechanisms underlying its flower development remain poorly understood. In this study, an integrated multi-omics strategy—combining transcriptome, sRNAome, and degradome sequencing—was employed to analyze three key stages of petal coloration (young bud, coloration initiation, and big bud) in the pink-flowered strawberry cultivar 'Sijihong'. The present analysis revealed dynamic transcriptional reprogramming primarily governed by hormone-signaling transcription factors (TFs), among which ERFs (<italic>AIL1</italic>), and bHLHs (<italic>bHLH93-like</italic>) were identified as central regulatory components. Importantly, extensive post-transcriptional regulation was uncovered, which is mediated by 151 conserved, and 38 novel miRNAs, and contributes to petal development. Among these regulatory mechanisms, the repression of SPL transcription factors by FamiR156 and the triggering of phasiRNA production from the auxin receptor gene <italic>FvAFB2</italic> by FvmiR393 are included. Additionally, 237 phasiRNA-producing loci (PHAS) were mapped, and these loci exhibit stage-specific expression patterns during floral maturation. This study delineates a hierarchical regulatory network that integrates transcriptional control, miRNA-guided silencing, and phasiRNA-mediated amplification to coordinate flower development, thereby offering valuable mechanistic insights and genetic resources for future horticultural improvement.