{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T13:57:17Z","timestamp":1792591037065,"version":"4.5.0"},"reference-count":51,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T00:00:00Z","timestamp":1762387200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Guizhou Association for Science and Technology \u201cXinzhi Qianyan\u201d Leading Project","award":["2025XZQYXM-01-27"],"award-info":[{"award-number":["2025XZQYXM-01-27"]}]},{"name":"Zunyi Science and Technology Plant Project","award":["Zunshikehe HZ Zi[2024]No.156"],"award-info":[{"award-number":["Zunshikehe HZ Zi[2024]No.156"]}]},{"name":"Zunyi Science and Technology Innovation Talent Team Project","award":["Zunshike Talent[2024]No.3"],"award-info":[{"award-number":["Zunshike Talent[2024]No.3"]}]},{"name":"2024 Guizhou Provincial Employee Innovation Grant Project"},{"name":"Zunyi Vocational and Technical College High-Level Talents Research Startup Fund Project","award":["Zunzhike Talent[2025]No.3"],"award-info":[{"award-number":["Zunzhike Talent[2025]No.3"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Lonicera macranthoides (L. macranthoides) is a traditional Chinese medicinal plant, the flower buds of which are rich in bioactive compounds, such as chlorogenic acids (CGAs) and flavonoids, and exhibit diverse pharmacological activities. Methods: Integrated transcriptomic and metabolomic analyses were conducted across three floral developmental stages: flower bud (FB), white flower (WF), and golden flower (GF). Results: Clustering analysis revealed distinct molecular profiles, with the WF and GF stages clustering together and clearly separating from the FB stage. The most significant metabolomic variation was observed between the GF and FB stages. KEGG enrichment analysis consistently highlighted the phenylpropanoid biosynthesis pathway as a key hub. Stage-specific accumulation patterns were identified for critical metabolites: caffeoylquinic acid peaked at the WF stage, while ferulic acid, sinapic acid, cinnamic acid, and p-coumaric acid reached their highest levels at the GF stage. Within this pathway, we identified 11 DEGs encoding the core enzymes, alongside 15 associated DAMs. The expression trends of four PAL genes were fully consistent with the accumulation of related precursors, and F5H expression correlated with its downstream product, sinapic acid. WGCNA identified a key module highly correlated with key phenolic acids, containing 71 transcription factors, including MYB, bHLH, WRKY, and AP2\/ERF families, potentially forming a complex regulatory network for phenylpropanoid biosynthesis. Conclusions: This study deciphers the stage-specific regulatory network of CGA biosynthesis, providing critical insights and genetic resources for cultivating high-medicinal-content varieties of L. macranthoides.<\/jats:p>","DOI":"10.3390\/genes16111339","type":"journal-article","created":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T17:51:43Z","timestamp":1762451503000},"page":"1339","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated Transcriptomic and Metabolomic Analyses Reveal Key Genes Involved in Phenylpropanoid Metabolism in Lonicera macranthoides Flowers"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8636-3328","authenticated-orcid":false,"given":"Zhengchun","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Conservation, Development and Utilization of Karst Characteristic Biological Resources, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi 563006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Institute for Forest Resources & Environment of Guizhou\/College of Forestry, Guizhou University, Guiyang 550025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hua","family":"Feng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Conservation, Development and Utilization of Karst Characteristic Biological Resources, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi 563006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Conservation, Development and Utilization of Karst Characteristic Biological Resources, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi 563006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaohua","family":"Zeng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Conservation, Development and Utilization of Karst Characteristic Biological Resources, Department of Modern Agriculture, Zunyi Vocational and Technical College, Zunyi 563006, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiandong","family":"Hou","sequence":"additional","affiliation":[{"name":"School of Ethnic-Minority Medicine, Guizhou Minzu University, Guiyang 550025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luonan","family":"Shen","sequence":"additional","affiliation":[{"name":"Institute for Forest Resources & Environment of Guizhou\/College of Forestry, Guizhou University, Guiyang 550025, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Liu, Q., Yu, H., Dong, Y., Quan, W., Su, Z., and Li, L. 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