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In this study, using integrated morphological, transcriptomic, and metabolomic analyses of R. coccinea, we found that the cell types of the dorsal and lateral perianth organs were broadly similar but clearly distinct from those of the lip and the column. Developmentally, the organ-specific expression patterns of AGAMOUS-LIKE6-1\/2 (AGL6-1\/2), APETALA3-1\/2 (AP3-1\/2), and AGAMOUS (AG) were consistent with the conserved orchid floral organ identity model. Furthermore, lip-enriched expression of brassinosteroid-responsive RING H2 (BRH1) and flavin-containing monooxygenase YUCCA10 (YUC10) suggests that brassinosteroid- and auxin-associated pathways may contribute to lip specialization, especially spur development. Regarding pigmentation, high expression of flavonoid 3\u2032-hydroxylase (F3\u2032H) was associated with a cyanidin-dominated anthocyanin profile. The color divergence among the dorsal sepal, petals, and lateral sepals was associated with differential expression of UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT), which was co-expressed with plant U-box protein 9 (PUB9) and carbon catabolite repressor 4 (CCR4), associated with distinct patterns of pigment modifications. These findings provide a molecular framework for understanding floral organ development and color patterning in R. coccinea and candidate genes for future validation and molecular breeding in Renanthera.<\/jats:p>","DOI":"10.3390\/biology15171497","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T10:02:52Z","timestamp":1788343372000},"page":"1497","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Multi-Omics Analysis Provides Insights into Floral Organ Development and Flower Color Formation in Renanthera coccinea, a Rare Tropical Orchid"],"prefix":"10.3390","volume":"15","author":[{"given":"Xin","family":"Yang","sequence":"first","affiliation":[{"name":"Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572025, China"},{"name":"The Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, National Germplasm Resource Chengmai Observation and Experiment Station, Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China"},{"name":"School of Tropical Agriculture and Forestry, Hainan University, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Lin","sequence":"additional","affiliation":[{"name":"Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572025, China"},{"name":"The Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, National Germplasm Resource Chengmai Observation and Experiment Station, Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572025, China"},{"name":"The Key Laboratory of Tropic Special Economic Plant 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China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sai","family":"Huang","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, National Germplasm Resource Chengmai Observation and Experiment Station, Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingfei","family":"Wang","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Tropic Special Economic Plant Innovation and Utilization, National Germplasm Resource Chengmai Observation and Experiment Station, Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuan","family":"Chen","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Tropic Special Economic Plant Innovation and 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