{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T08:31:00Z","timestamp":1765873860865,"version":"3.48.0"},"reference-count":47,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T00:00:00Z","timestamp":1765843200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Xishuangbanna Prefecture Science and Technology Plan Project","award":["No. 202401001"],"award-info":[{"award-number":["No. 202401001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      The dried root of\n                      <jats:italic>Gongronemopsis tenacissima<\/jats:italic>\n                      (Roxb.) S. Reuss, Liede &amp; Meve, traditionally known as Dai-Bai-Jie, is a medicinal plant used by the Dai ethnic group, primarily for detoxification. Due to extensive use, wild resources have become increasingly scarce, prompting domestication efforts in China. However, the accumulation patterns of secondary metabolites\u2014particularly flavonoids, the main detoxifying components\u2014and their biosynthetic mechanisms remain unclear.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study investigated differences in flavonoid accumulation and transcriptional regulation in Dai-Bai-Jie cultivated for one, two, and three years at high altitudes, and three years at low altitudes. Transcriptome and widely targeted metabolome analyses were conducted. A total of 1,495 metabolites were identified using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS\/MS), with 943 showing differential accumulation across the four groups. All flavonoids were classified into six clusters using k-means clustering. Flavonoid levels were generally higher in plants cultivated for two and three years, with total metabolite content also more abundant in these groups. Two-year cultivation was recommended as the optimal harvesting strategy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>A regulatory relationship was observed between genes such as phenylalanine ammonia-lyase, CYP73A, 4-coumarate: coenzyme A ligase, and flavonol synthase, and the flavonoid components in Dai-Bai-Jie. No significant differences were found in Shannon, Chao1, or abundance coverage estimator (ACE) indices of rhizosphere microorganisms across different cultivation years and locations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>This study elucidates the mechanisms of flavonoid accumulation and supports the scientific rationale for optimal harvesting years of Dai-Bai-Jie. The findings provide a valuable foundation for guiding large-scale cultivation and reducing reliance on wild resources.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.7717\/peerj.20439","type":"journal-article","created":{"date-parts":[[2025,12,16]],"date-time":"2025-12-16T08:28:33Z","timestamp":1765873713000},"page":"e20439","source":"Crossref","is-referenced-by-count":0,"title":["Multiomics analysis reveals flavonoid accumulation and biosynthesis across different cultivation years and localities of\n                    <i>Gongronemopsis tenacissima<\/i>\n                    (Dai-Bai-Jie)"],"prefix":"10.7717","volume":"13","author":[{"given":"Mengqi","family":"Wang","sequence":"first","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunxia","family":"Gu","sequence":"additional","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liming","family":"Shan","sequence":"additional","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunyu","family":"Li","sequence":"additional","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ertai","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ge","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoli","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2025,12,16]]},"reference":[{"key":"10.7717\/peerj.20439\/ref-1","doi-asserted-by":"publisher","first-page":"116961","DOI":"10.1016\/j.biopha.2024.116961","article-title":"Pharmacological insight of rutin as a potential candidate against peptic ulcer","volume":"177","author":"Akash","year":"2024","journal-title":"Biomedicine & Pharmacotherapy"},{"issue":"20","key":"10.7717\/peerj.20439\/ref-2","doi-asserted-by":"publisher","first-page":"84","DOI":"10.4103\/0973-7847.194044","article-title":"Overviews of biological importance of quercetin: a bioactive flavonoid","volume":"10","author":"Anand\u00a0David","year":"2016","journal-title":"Pharmacognosy Reviews"},{"issue":"6","key":"10.7717\/peerj.20439\/ref-3","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1007\/s12298-023-01329-1","article-title":"Two monolignoid biosynthetic genes, 4-coumarate: coenzyme A ligase (4CL) and p-coumaric acid 3-hydroxylase (C3H) involved in lignin accumulation in pear fruits","volume":"29","author":"Cao","year":"2023","journal-title":"Physiology and Molecular Biology of Plants"},{"key":"10.7717\/peerj.20439\/ref-4","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/j.jnutbio.2015.09.016","article-title":"Molecular mechanisms of gastrointestinal protection by quercetin against indomethacin-induced damage: role of NF-\u03baB and Nrf2","volume":"27","author":"Catalina","year":"2016","journal-title":"The Journal of Nutritional Biochemistry"},{"key":"10.7717\/peerj.20439\/ref-5","doi-asserted-by":"publisher","first-page":"115381","DOI":"10.1016\/j.jep.2022.115381","article-title":"Marsdenia tenacissima (Roxb.) 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