{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:44:00Z","timestamp":1787028240591,"version":"build-2736575974"},"reference-count":40,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:00:00Z","timestamp":1772150400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Natural Science Research Project of Anhui Provincial Department of Education","award":["2025AHGXZK40428"],"award-info":[{"award-number":["2025AHGXZK40428"]}]},{"name":"Open Fund of Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration","award":["2025KYPT07"],"award-info":[{"award-number":["2025KYPT07"]}]},{"name":"Key Special Project of the Science and Technology Program of Suzhou","award":["SZKJXM202423"],"award-info":[{"award-number":["SZKJXM202423"]}]},{"name":"Doctoral Research Startup Foundation Project of Suzhou University","award":["2022BSK033"],"award-info":[{"award-number":["2022BSK033"]}]},{"name":"National and Provincial College Students\u2019 Innovation and Entrepreneurship Training Program Project funded by Suzhou University","award":["202510379040"],"award-info":[{"award-number":["202510379040"]}]},{"name":"National and Provincial College Students\u2019 Innovation and Entrepreneurship Training Program Project funded by Suzhou University","award":["S202510379134"],"award-info":[{"award-number":["S202510379134"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Salvia miltiorrhiza (Danshen) is a well-known medicinal herb in traditional Chinese medicine. It produces tanshinones and salvianolic acids as key bioactive constituents in its roots, yet the molecular basis for their tissue-specific accumulation is still poorly understood. This study aims to identify candidate functional genes involved in the biosynthesis of tanshinones and salvianolic acids, and to reveal the molecular basis underlying their tissue-specific accumulation in S. miltiorrhiza. Methods: For this purpose, we compared transcriptomic and metabolomic differences between the roots and leaves, and further measured a set of physiological parameters, including the POD, SOD, CAT and PAL activities, as well as the total phenols and flavones contents. Results: Metabolomic analysis identified 6805 metabolites, of which 241 were differentially accumulated between roots and leaves, with 172 upregulated in roots. The elevated metabolites included gibberellin, cryptotanshinone, decursinol angelate, chalcone, and psoralenol. Transcriptome analysis identified 32,700 annotated genes, with 9895 showing differential expression between roots and leaves, including 4199 upregulated in roots. Roots exhibited higher levels of phenols and flavones, as well as significantly greater POD, SOD, CAT, and PAL activities. Conclusions: Integrated omics analysis identified putative candidate genes including CPS, KS, and P450s as potential contributors for tanshinone and salvianolic acid biosynthesis. The identified genes provide valuable resources for molecular breeding, offering opportunities to improve the medicinal quality of S. miltiorrhiza.<\/jats:p>","DOI":"10.3390\/genes17030280","type":"journal-article","created":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T15:52:38Z","timestamp":1772207558000},"page":"280","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Transcriptome and Metabolome-Based Analysis Reveals the Molecular Mechanisms Underlying the Differences in Tanshinone and Salvianolic Acid Content Between Salvia miltiorrhiza Roots and Leaves"],"prefix":"10.3390","volume":"17","author":[{"given":"Fawang","family":"Liu","sequence":"first","affiliation":[{"name":"School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou 234000, China"},{"name":"Anhui Engineering Laboratory for Medicinal and Food Homologous Natural Resources Exploration, Hefei Normal University, Hefei 230601, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingying","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou 234000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou 234000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yin","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou 234000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengping","family":"Ding","sequence":"additional","affiliation":[{"name":"School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou 234000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1002\/med.21304","article-title":"The anticancer properties of Salvia miltiorrhiza Bunge (Danshen): A systematic review","volume":"34","author":"Chen","year":"2014","journal-title":"Med. 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