biostudies-literatureUnknown16(5)Fu JSystems-wide understanding of gene expression profile regulating flower colour formation in <i>Rhododendron simsii</i> Planchon is insufficient. In this research, integration analysis of ribonucleic acid (RNA)omics and microRNAome were performed to reveal the molecular mechanism of flower colour formation in three <i>R. simsii</i> varieties with red, pink and crimson flowers, respectively. Totally, 3129, 5755 and 5295 differentially expressed gene (DEG)s were identified through comparative transcriptome analysis between 'Red variety' and 'Pink variety' (1507 up-regulated and 1622 down-regulated), 'Red variety' and 'Crimson variety' (2148 up-regulated 3607 down-regulated), as well as 'Pink variety' and 'Crimson variety' (2089 up-regulated and 3206 down-regulated), which were involved in proAoB PLANTSplae053https://www.ebi.ac.uk/biostudies/studies/S-EPMC11489732biostudies-literatureMolecular mechanism of flower colour formation in <i>Rhododendron simsii</i> Planchon revealed by integration of microRNAome and RNAomics.PMC11489732Zhang JWang SFu JTian CWan XYu JHu RfalseMolecular mechanism of flower colour formation in <i>Rhododendron simsii</i> Planchon revealed by integration of microRNAome and RNAomics.Systems-wide understanding of gene expression profile regulating flower colour formation in <i>Rhododendron simsii</i> Planchon is insufficient. In this research, integration analysis of ribonucleic acid (RNA)omics and microRNAome were performed to reveal the molecular mechanism of flower colour formation in three <i>R. simsii</i> varieties with red, pink and crimson flowers, respectively. Totally, 3129, 5755 and 5295 differentially expressed gene (DEG)s were identified through comparative transcriptome analysis between 'Red variety' and 'Pink variety' (1507 up-regulated and 1622 down-regulated), 'Red variety' and 'Crimson variety' (2148 up-regulated 3607 down-regulated), as well as 'Pink variety' and 'Crimson variety' (2089 up-regulated and 3206 down-regulated), which were involved in pro2024-01-01T00:00:00Z2024 Oct2026-06-03T07:18:12.853Z2025-04-06T09:35:03.39ZS-EPMC114897323943043710.1093/aobpla/plae053