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Recently, a novel, more resistant variant called\n                    <jats:italic>L. brownii<\/jats:italic>\n                    var.\n                    <jats:italic>viridulum<\/jats:italic>\n                    (Xuefeng, xf) was identified through individual plant selection. However, the metabolic and transcriptional profiles of xf, particularly concerning flavonoid metabolism, have not yet been compared to those of the traditional variant (Longya, ly). To address this gap, we performed an integrated metabolomic and transcriptomic analysis to systematically compare flavonoid metabolism between ly and xf. Our metabolomic analysis identified 85 flavonoids that are significantly enriched in the xf variety. In the transcriptomic analysis, we identified 59 differentially expressed enzyme genes, with expression levels in xf being significantly higher than those in ly, consistent with the metabolite profile. By combining transcriptome and metabolome, we identified one MYB transcription factor (Cluster-6560.0) and four bHLH transcription factors (Cluster-22934.6, Cluster-22934.10, Cluster-24120.2, and Cluster-24120.13) linked to anthocyanin synthesis. The co-expression of these identified genes supports the enrichment of flavonoids in xf, and this coordinated expression pattern of key enzymes was further confirmed via real-time quantitative PCR (qRT-PCR). In conclusion, this study enhances our understanding of the molecular mechanisms underlying flavonoid biosynthesis and provides a strong foundation for the genetic breeding of lilies.\n                  <\/jats:p>","DOI":"10.1038\/s41598-026-43274-5","type":"journal-article","created":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T06:05:40Z","timestamp":1773727540000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative metabolomic and transcriptomic profiling deciphers flavonoid biosynthesis of bulbs in Lilium brownii var. Viridulum"],"prefix":"10.1038","volume":"16","author":[{"given":"Pu-Tao","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Jie","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"You","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin-Fang","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,3,17]]},"reference":[{"key":"43274_CR1","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.3390\/ph17091242","volume":"17","author":"Y Wang","year":"2024","unstructured":"Wang, Y. et al. 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No endangered or protected species were used in this study. And the lily germplasm resource nursery in Beidouxi Town, Xupu County, Huaihua City, Hunan Province, China (110\u00b032\u20326.8175\u2033E, 27\u00b039\u203211.7432\u2033N), was jointly established by local lily growers and the Key Laboratory of Dong Medical Research of Hunan Province, where we are affiliated. Sample collection was carried out with permission from both parties.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}],"article-number":"13814"}}