{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:34:33Z","timestamp":1785803673010,"version":"3.56.0"},"reference-count":45,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005892","name":"China Academy of Chinese Medical Sciences","doi-asserted-by":"crossref","award":["ZZ2024036"],"award-info":[{"award-number":["ZZ2024036"]}],"id":[{"id":"10.13039\/501100005892","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005892","name":"China Academy of Chinese Medical Sciences","doi-asserted-by":"crossref","award":["ZK2024010"],"award-info":[{"award-number":["ZK2024010"]}],"id":[{"id":"10.13039\/501100005892","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005892","name":"China Academy of Chinese Medical Sciences","doi-asserted-by":"crossref","award":["ZA2025021"],"award-info":[{"award-number":["ZA2025021"]}],"id":[{"id":"10.13039\/501100005892","id-type":"DOI","asserted-by":"crossref"}]},{"award":["ZZ2024036"],"award-info":[{"award-number":["ZZ2024036"]}],"id":[{"id":"https:\/\/ror.org\/042pgcv68","id-type":"ROR","asserted-by":"publisher"}]},{"award":["ZK2024010"],"award-info":[{"award-number":["ZK2024010"]}],"id":[{"id":"https:\/\/ror.org\/042pgcv68","id-type":"ROR","asserted-by":"publisher"}]},{"award":["ZA2025021"],"award-info":[{"award-number":["ZA2025021"]}],"id":[{"id":"https:\/\/ror.org\/042pgcv68","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFC3503801"],"award-info":[{"award-number":["2023YFC3503801"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"China Agriculture Research System of MOF and MARA","award":["CARS-21"],"award-info":[{"award-number":["CARS-21"]}]},{"award":["CARS-21"],"award-info":[{"award-number":["CARS-21"]}],"id":[{"id":"https:\/\/ror.org\/03p5eky76","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Metabolites"],"abstract":"<jats:p>Background\/Objective:\u00a0Anoectochilus roxburghii, a high-value medicinal orchid, faces significant challenges in quality standardization during large-scale tissue culture due to a lack of understanding of the underlying molecular mechanisms. This study aimed to compare \u201cJianlan No.2\u201d plantlets cultured under a conventional tissue culture system (CK) and a sugar-free tissue culture system (TD), to elucidate the phenotypic and molecular basis for quality improvement. Methods: A systematic comparison was conducted. Phenotypic traits of plantlets from both systems were measured. Integrated transcriptomic (RNA sequencing) and untargeted metabolomic analyses were employed to identify the molecular differences at the gene expression and metabolite accumulation levels. Results: TD-grown seedlings exhibited significantly superior growth characteristics, including greater plant height, higher rooting rate, and improved transplant survival. Transcriptomic analysis identified 416 differentially expressed genes (DEGs) (44 upregulated, 372 downregulated in TD), which were significantly enriched in pathways related to cell wall organization, apoplast, and photosynthesis. Sixteen key genes were pinpointed as closely associated with seedling growth and metabolic regulation. Metabolomic profiling revealed 502 differentially accumulated metabolites (DAMs), with significant perturbations primarily in phenylpropanoid biosynthesis and terpenoid metabolism. Conclusions: The sugar-free tissue culture system enhances A. roxburghii seedling quality by coordinately modulating photosynthetic capacity, carbon metabolism, and the biosynthesis of key secondary metabolites. These findings provide a crucial molecular foundation for optimizing tissue culture protocols and advancing the standardized, high-quality cultivation of this valuable medicinal plant.<\/jats:p>","DOI":"10.3390\/metabo16060374","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T17:36:18Z","timestamp":1780076178000},"page":"374","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptomic and Metabolomic Insights into the Enhanced Quality of Anoectochilus roxburghii Seedlings in Sugar-Free Versus Conventional Tissue Culture Systems"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2758-4785","authenticated-orcid":false,"given":"Chuanzhi","family":"Kang","sequence":"first","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tongwei","family":"Lin","sequence":"additional","affiliation":[{"name":"Lishui Jianlan Biotechnology Co., Ltd., Lishui 323500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyang","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiheng","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9381-0751","authenticated-orcid":false,"given":"Dehua","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanying","family":"Duan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zekun","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7983-3229","authenticated-orcid":false,"given":"Chengcai","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangtao","family":"Chen","sequence":"additional","affiliation":[{"name":"Lishui Jianlan Biotechnology Co., Ltd., Lishui 323500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangfang","family":"Chen","sequence":"additional","affiliation":[{"name":"Hangzhou Mumu Biotechnology Co., Ltd., Hangzhou 311300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.jep.2017.07.032","article-title":"Anoectochilus roxburghii: A review of its phytochemistry, pharmacology, and clinical applications","volume":"209","author":"Ye","year":"2017","journal-title":"J. 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