{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T09:17:43Z","timestamp":1787735863018,"version":"build-2784847793"},"reference-count":35,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Technological Innovation Project of Hainan Provincial Research Institutes","award":["KYYSLK2023-007"],"award-info":[{"award-number":["KYYSLK2023-007"]}]},{"award":["KYYSLK2023-007"],"award-info":[{"award-number":["KYYSLK2023-007"]}],"id":[{"id":"https:\/\/ror.org\/045n75910","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Flower color is a core ornamental trait in orchids (Orchidaceae), arising from the biosynthesis, accumulation, and spatial distribution of pigments under multilayered transcriptional regulation. Methods: We performed parallel RNA-seq transcriptomic and widely targeted metabolomic profiling of 15 samples representing five floral tissue\/color categories from an F1 population of Cymbidium eburneum (\u2018Duzhan Chun\u2019) \u00d7 Cymbidium insigne (\u2018Meihua Lan\u2019). Results: Across four prespecified pairwise comparisons, 4891 non-redundant differentially expressed genes (DEGs) and 383 non-redundant differentially accumulated metabolites (DAMs) were identified. WGCNA resolved 12 co-expression modules. Recalculation from archived files identified darkseagreen4 as the module most positively associated with red tissues (r = 0.888), lightgreen as the module most positively associated with yellow tissues (r = 0.916), and plum1 as the module most strongly associated with white tissues in the negative direction (r = \u22120.983). Genes meeting |MM| \u2265 0.80, |GS| \u2265 0.80, MM p &lt; 0.01, and GS p &lt; 0.01 were retained as color-associated candidates. Anthocyanin derivatives including Cyanidin-3-O-sambubioside-5-O-glucoside, Delphinidin-3-rutinoside, and Peonidin-3,5-O-di-\u03b2-glucoside were associated with red floral tissues. Conclusions: Integrated analyses consistently highlighted phenylpropanoid and flavonoid biosynthesis, whereas isoquinoline alkaloid enrichment remains hypothesis-generating. These associations nominate candidates but do not establish causal pigmentation regulators.<\/jats:p>","DOI":"10.3390\/genes17091003","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T08:11:15Z","timestamp":1787731875000},"page":"1003","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Multi-Omics Analysis Reveals Key Metabolites and Regulatory Networks Underlying Flower Color Variation in F1 Hybrids of Cymbidium eburneum \u00d7 Cymbidium insigne"],"prefix":"10.3390","volume":"17","author":[{"given":"Yu","family":"Han","sequence":"first","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutong","family":"Cui","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Chen","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dandan","family":"Rao","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erhuan","family":"Wu","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rongcun","family":"Gan","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tengmin","family":"Li","sequence":"additional","affiliation":[{"name":"Forestry High-Tech Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China"},{"name":"The Innovation Platform for Academicians of Hainan Province, Haikou 571100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"201","DOI":"10.11646\/phytotaxa.261.3.1","article-title":"The number of known plant species in the world and its annual increase","volume":"261","author":"Christenhusz","year":"2016","journal-title":"Phytotaxa"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"20151553","DOI":"10.1098\/rspb.2015.1553","article-title":"Orchid phylogenomics and multiple drivers of their extraordinary diversification","volume":"282","author":"Givnish","year":"2015","journal-title":"Proc. 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