{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:45:44Z","timestamp":1785422744018,"version":"3.56.0"},"reference-count":87,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100014978","name":"Undergraduate Research and Innovation Project of Hunan University of Chinese Medicine","doi-asserted-by":"publisher","award":["2024BKS079"],"award-info":[{"award-number":["2024BKS079"]}],"id":[{"id":"10.13039\/501100014978","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2024BKS079"],"award-info":[{"award-number":["2024BKS079"]}],"id":[{"id":"https:\/\/ror.org\/05htk5m33","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Undergraduate Innovation Training Project of Hunan Province","award":["S202310541092"],"award-info":[{"award-number":["S202310541092"]}]},{"name":"First-Class Discipline of Pharmaceutical Science of Hunan"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Kadsura heteroclita (Roxb.) Craib, commonly known as \u201cXuetong\u201d, is a traditional Tujia ethnomedicine with anti-rheumatoid arthritis (RA) activity, and schizanlactone E (Xuetongsu) is its major bioactive component whose biosynthetic pathway remains uncharacterized. As a cycloartane-type tetracyclic triterpenoid, Xuetongsu\u2019s biosynthesis is likely to involve multiple oxidation steps. Cytochrome P450 (CYP450) is a versatile monooxygenase encoded by a large and diverse gene superfamily and plays a critical role in various oxidation reactions in plants\u2019 secondary metabolism. In this study, 367 KhCYP450s were identified and systematically analyzed for their physicochemical properties, phylogenetic analysis, conserved motifs, gene structures, collinearity, and cis-acting elements. Weighted gene co-expression network analysis (WGCNA) revealed a turquoise module strongly associated with Xuetong root tissue, which had the highest Xuetongsu accumulation; 32 candidate KhCYP450s within this module were screened via correlation analysis between gene expression and xuetongsu content and partially validated by qRT-PCR. Five of these candidates showed significant homology with known triterpenoid biosynthetic genes via protein structure analyses. This study deepened our comprehension of the CYP450 superfamily in Xuetong and provided a valuable reference for further research on the biosynthesis of Xuetongsu.<\/jats:p>","DOI":"10.3390\/molecules31122140","type":"journal-article","created":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T15:11:22Z","timestamp":1781709082000},"page":"2140","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Insights into the Cytochrome P450 Monooxygenase Superfamily in Kadsura heteroclita (Xuetong)"],"prefix":"10.3390","volume":"31","author":[{"given":"Qian","family":"Xiao","sequence":"first","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianhao","family":"Fu","sequence":"additional","affiliation":[{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mao","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyi","family":"Cai","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiahui","family":"Yi","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengqin","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenni","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chensi","family":"Tan","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiang","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0876-2205","authenticated-orcid":false,"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7188-3144","authenticated-orcid":false,"given":"Luyun","family":"Ning","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China"},{"name":"Traditional Chinese Medicine (TCM) and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,17]]},"reference":[{"key":"ref_1","first-page":"173","article-title":"The Research Progress of Plant Cytochrome P450 Family","volume":"42","author":"Cui","year":"2020","journal-title":"Chin. J. Grassl."},{"key":"ref_2","first-page":"5597","article-title":"Research progress on CYP450 involved in medicinal plant triterpenoid biosynthesis","volume":"50","author":"Zhu","year":"2019","journal-title":"Chin. Tradit. Herb. Drugs"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1146\/annurev.arplant.49.1.311","article-title":"Molecular-genetic analysis of plant cytochrome P450-dependent monooxygenases","volume":"49","author":"Chapple","year":"1998","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1248\/bpb.35.824","article-title":"Impacts of diversification of cytochrome P450 on plant metabolism","volume":"35","author":"Mizutani","year":"2012","journal-title":"Biol. Pharm. Bull."},{"key":"ref_5","first-page":"2176","article-title":"Advances of Cytochrome P450s in the Biosynthesis of Plant Secondary Metabolites","volume":"22","author":"Li","year":"2024","journal-title":"Mol. Plant Breed."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1111\/j.1365-313X.2011.04529.x","article-title":"A P450-centric view of plant evolution","volume":"66","author":"Nelson","year":"2011","journal-title":"Plant J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/00008571-199602000-00002","article-title":"P450 superfamily: Update on new sequences, gene mapping, accession numbers and nomenclature","volume":"6","author":"Nelson","year":"1996","journal-title":"Pharmacogenetics"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4619","DOI":"10.1093\/jxb\/erz203","article-title":"Research advances in cytochrome P450-catalysed pharmaceutical terpenoid biosynthesis in plants","volume":"70","author":"Zheng","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1515\/DMDI.1995.12.3-4.189","article-title":"Diversity and evolution of plant P450 and P450-reductases","volume":"12","author":"Durst","year":"1995","journal-title":"Drug Metab. Drug Interact."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Guttikonda, S.K., Trupti, J., Bisht, N.C., Chen, H., An, Y.-Q.C., Pandey, S., Xu, D., and Yu, O. (2010). Whole genome co-expression analysis of soybean cytochrome P450 genes identifies nodulation-specific P450 monooxygenases. BMC Plant Biol., 10.","DOI":"10.1186\/1471-2229-10-243"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"uhac283","DOI":"10.1093\/hr\/uhac283","article-title":"Genome-wide analysis of cytochrome P450 genes in Citrus clementina and characterization of a CYP gene encoding flavonoid 3\u2032-hydroxylase","volume":"10","author":"Liu","year":"2023","journal-title":"Hortic. Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.pbiomolbio.2024.09.003","article-title":"Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response","volume":"193","author":"Mokhosoev","year":"2024","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_13","unstructured":"The UniProt Consortium (2024). UniProt: The Universal Protein Knowledgebase in 2025. Nucleic Acids Res., 53, D609\u2013D617."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1016\/j.molp.2021.06.028","article-title":"Plant cytochrome P450 plasticity and evolution","volume":"14","author":"Hansen","year":"2021","journal-title":"Mol. Plant"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"152876","DOI":"10.1016\/j.phymed.2019.152876","article-title":"Kadsura heteroclita stem suppresses the onset and progression of adjuvant-induced arthritis in rats","volume":"58","author":"Yu","year":"2019","journal-title":"Phytomedicine"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1016\/j.jep.2016.11.011","article-title":"Effects of the stem extracts of Schisandra glaucescens Diels on collagen-induced arthritis in Balb\/c mice","volume":"194","author":"Xiang","year":"2016","journal-title":"J. Ethnopharmacol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"319","DOI":"10.38212\/2224-6614.3348","article-title":"Simultaneously qualitative and quantitative analysis of the representative components in Kadsura heteroclita stem by UHPLC-Q-Orbitrap HRMS","volume":"29","author":"Liu","year":"2021","journal-title":"J. Food Drug Anal."},{"key":"ref_18","first-page":"121","article-title":"Summary on Source and Pharmacological Effects of Tujia Ethnomedicine \u2018Blood\u2019 Drugs","volume":"39","author":"Xie","year":"2019","journal-title":"J. Hunan Univ. Chin. Med."},{"key":"ref_19","first-page":"1","article-title":"Research on the Tujia ethnomedicine \u201cseven\u201d drugs","volume":"35","author":"Shen","year":"2015","journal-title":"J. Hunan Univ. Chin. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"111902","DOI":"10.1016\/j.jep.2019.111902","article-title":"Analgesic and anti-inflammatory effects and molecular mechanisms of Kadsura heteroclita stems, an anti-arthritic Chinese Tujia ethnomedicinal herb","volume":"238","author":"Yu","year":"2019","journal-title":"J. Ethnopharmacol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Wang, M.Y., Jiang, S., Hussain, N., Zafar, S., Xie, Q.L., Huang, F.B., Mao, L.X., Li, B., Jian, Y.Q., and Wang, W. (2022). Anti-RAFLS triterpenoids and Hepatoprotective Lignans from the leaves of Tujia Ethnomedicine Kadsura heteroclita (Xuetong). Front. Chem., 10.","DOI":"10.3389\/fchem.2022.878811"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/S2589-3777(19)30032-1","article-title":"A review of triterpenoids and their pharmacological activities from genus Kadsura","volume":"1","author":"Liu","year":"2018","journal-title":"Digit. Chin. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"113567","DOI":"10.1016\/j.jep.2020.113567","article-title":"A review of the phytochemistry and pharmacology of Kadsura heteroclita, an important plant in Tujia ethnomedicine","volume":"268","author":"Wang","year":"2021","journal-title":"J. Ethnopharmacol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1055\/s-2005-916263","article-title":"New triterpenoids from Kadsura heteroclita and their cytotoxic activity","volume":"72","author":"Wang","year":"2006","journal-title":"Planta Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1002\/mrc.2000","article-title":"Structural determination of seven new triterpenoids from Kadsura heteroclita by NMR techniques","volume":"45","author":"Wang","year":"2007","journal-title":"Magn. Reson. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2289","DOI":"10.1002\/cbdv.200900173","article-title":"Bioactive triterpenoids from Kadsura heteroclita","volume":"7","author":"Xu","year":"2010","journal-title":"Chem. Biodivers."},{"key":"ref_27","first-page":"689","article-title":"Heteroclitins RS: New dibenzocylooctadiene lignans from Kadsura heteroclita","volume":"12","author":"Chen","year":"2014","journal-title":"Chin. J. Nat. Med."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Cao, L., Shehla, N., Tasneem, S., Cao, M., Sheng, W., Jian, Y.Q., Li, B., Peng, C.Y., Choudhary, M.I., and Liao, D.F. (2019). New cadinane sesquiterpenes from the stems of Kadsura heteroclita. Molecules, 24.","DOI":"10.3390\/molecules24091664"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1021\/acsnano.1c07556","article-title":"Biomimetic hybrid membrane-coated xuetongsu assisted with laser irradiation for efficient rheumatoid arthritis therapy","volume":"16","author":"Yu","year":"2022","journal-title":"ACS Nano"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"23345","DOI":"10.1038\/s41598-024-73471-z","article-title":"Effective extraction of Xuetongsu and its role in preventing RA synovial hyperplasia by targeting synovial cell migration and apoptosis","volume":"14","author":"Deng","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1146\/annurev.arplant.54.031902.134840","article-title":"Functional genomics of P450s","volume":"54","author":"Schuler","year":"2003","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1002\/bit.26583","article-title":"Biosynthesis of a ganoderic acid in Saccharomyces cerevisiae by expressing a cytochrome P450 gene from Ganoderma lucidum","volume":"115","author":"Wang","year":"2018","journal-title":"Biotechnol. Bioeng."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s00253-021-11717-w","article-title":"Biosynthesis of a novel ganoderic acid by expressing CYP genes from Ganoderma lucidum in Saccharomyces cerevisiae","volume":"106","author":"Wang","year":"2022","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6367","DOI":"10.1038\/s41467-025-61686-1","article-title":"Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis","volume":"16","author":"Hakim","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1126\/science.adf1017","article-title":"Complex scaffold remodeling in plant triterpene biosynthesis","volume":"379","author":"Hodgson","year":"2023","journal-title":"Science"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1826","DOI":"10.1038\/s41477-024-01827-4","article-title":"Total biosynthesis of the medicinal triterpenoid saponin astragalosides","volume":"10","author":"Xu","year":"2024","journal-title":"Nat. Plants"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"iyae027","DOI":"10.1093\/genetics\/iyae027","article-title":"The Arabidopsis information resource in 2024","volume":"227","author":"Reiser","year":"2024","journal-title":"Genetics"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.3762\/bjoc.18.135","article-title":"Cytochrome P450 monooxygenase-mediated tailoring of triterpenoids and steroids in plants","volume":"18","author":"Malhotra","year":"2022","journal-title":"Beilstein J. Org. Chem."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Ghosh, S. (2017). Triterpene Structural Diversification by Plant Cytochrome P450 Enzymes. Front. Plant Sci., 8.","DOI":"10.3389\/fpls.2017.01886"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wei, K.F., and Chen, H.Q. (2018). Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice. BMC Genom., 19.","DOI":"10.1186\/s12864-017-4425-8"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Liu, J.W., Hu, H.M., Shen, H.M., Tian, Q.Y., Ding, W.J., Yang, X.L., Wang, L.G., and Yue, Y.Z. (2022). Insights into the cytochrome P450 monooxygenase superfamily in Osmanthus fragrans and the role of OfCYP142 in linalool synthesis. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232012150"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Liao, W.F., Zhao, S.Y., Zhang, M., Dong, K.G., Chen, Y., Fu, C.H., and Yu, L.J. (2017). Transcriptome assembly and systematic identification of novel cytochrome P450s in Taxus chinensis. Front. Plant Sci., 8.","DOI":"10.3389\/fpls.2017.01468"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1016\/j.tips.2016.05.006","article-title":"Recent structural insights into cytochrome P450 function","volume":"37","author":"Guengerich","year":"2016","journal-title":"Trends Pharmacol. Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e0144","DOI":"10.1199\/tab.0144","article-title":"Cytochromes P450","volume":"9","author":"Bak","year":"2011","journal-title":"Arab. Book"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/S0969-2126(01)00134-4","article-title":"Structure and function of cytochromes P450: A comparative analysis of three crystal structures","volume":"3","author":"Hasemann","year":"1995","journal-title":"Structure"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Kang, X.Y., Zhou, Y., Liu, Q., Liu, M., Chen, J., Zhang, Y.W., Wei, J., and Wang, Y. (2024). Characterization and expression of the cytochrome P450 genes in Daphnia magna exposed to cerium oxide nanoparticles. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms251910812"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Pandian, B.A., Sathishraj, R., Djanaguiraman, M., Prasad, P.V., and Jugulam, M. (2020). Role of cytochrome P450 enzymes in plant stress response. Antioxidants, 9.","DOI":"10.3390\/antiox9050454"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1016\/S2095-3119(14)60980-1","article-title":"The cytochrome P450 superfamily: Key players in plant development and defense","volume":"14","author":"Jun","year":"2015","journal-title":"J. Integr. Agric."},{"key":"ref_49","first-page":"1160","article-title":"CYP71D8L is a key regulator involved in growth and stress responses by mediating gibberellin homeostasis in rice","volume":"71","author":"Zhou","year":"2019","journal-title":"J. Exp. Bot."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1007\/s00425-022-03896-1","article-title":"Genome-wide transcriptome analysis and characterization of the cytochrome P450 flavonoid biosynthesis genes in pigeon pea (Cajanus cajan)","volume":"255","author":"Yang","year":"2022","journal-title":"Planta"},{"key":"ref_51","first-page":"682","article-title":"Selection and validation of reference genes for quantitative real-time PCR analysis in Tujia medicine Xuetong","volume":"50","author":"Xiao","year":"2025","journal-title":"Chin. J. Chin. Mater. Med."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"16116","DOI":"10.1073\/pnas.1109273108","article-title":"Formation of plant metabolic gene clusters within dynamic chromosomal regions","volume":"108","author":"Field","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"4112","DOI":"10.1105\/tpc.110.082685","article-title":"Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin","volume":"23","author":"Seki","year":"2011","journal-title":"Plant Cell"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1111\/j.1742-4658.2006.05120.x","article-title":"Identification of beta-amyrin and sophoradiol 24-hydroxylase by expressed sequence tag mining and functional expression assay","volume":"273","author":"Shibuya","year":"2006","journal-title":"FEBS J."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Chuang, L., Liu, S., Biedermann, D., and Franke, J. (2022). Identification of early quassinoid biosynthesis in the invasive tree of heaven (Ailanthus altissima) confirms evolutionary origin from protolimonoids. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.958138"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"17096","DOI":"10.1073\/pnas.1906083116","article-title":"Identification of key enzymes responsible for protolimonoid biosynthesis in plants: Opening the door to azadirachtin production","volume":"116","author":"Hodgson","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"D444","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: The protein sequence classification resource in 2025","volume":"53","author":"Blum","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: Interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","article-title":"The conserved domain database in 2023","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"D200","DOI":"10.1093\/nar\/gkw1129","article-title":"CDD\/SPARCLE: Functional classification of proteins via subfamily domain architectures","volume":"45","author":"Bo","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"W327","DOI":"10.1093\/nar\/gkh454","article-title":"CD-Search: Protein domain annotations on the fly","volume":"32","author":"Bryant","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"D225","DOI":"10.1093\/nar\/gkq1189","article-title":"CDD: A Conserved Domain Database for the functional annotation of proteins","volume":"39","author":"Lu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"W216","DOI":"10.1093\/nar\/gkab225","article-title":"Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users","volume":"49","author":"Duvaud","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"W215","DOI":"10.1093\/nar\/gkae237","article-title":"DeepLoc 2.1: Multi-label membrane protein type prediction using protein language models","volume":"52","author":"Teufel","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"6968","DOI":"10.1038\/s41467-022-34630-w","article-title":"Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny","volume":"13","author":"Edgar","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"W270","DOI":"10.1093\/nar\/gkz357","article-title":"Evolview v3: A webserver for visualization, annotation, and management of phylogenetic trees","volume":"47","author":"Subramanian","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"R24","DOI":"10.1186\/gb-2007-8-2-r24","article-title":"Quantifying similarity between motifs","volume":"8","author":"Gupta","year":"2007","journal-title":"Genome Biol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: A \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/nar\/30.1.325","article-title":"PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences","volume":"30","author":"Lescot","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Wang, J.X., Yang, B.P., Zhang, F.S., Wang, J.R., Xue, K., Hussain Chang, B., Zhang, J.Q., and Qin, X.M. (2024). Identification and Expression Analysis of Cytochrome P450 Genes Probably Involved in Triterpenoid Saponins Biosynthesis in Astragalus mongholicus. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25158333"},{"key":"ref_80","first-page":"2068","article-title":"Genome-wide transcriptome analysis reveals the regulatory network governing terpene trilactones biosynthesis in Ginkgo biloba","volume":"42","author":"Ye","year":"2022","journal-title":"Tree Physiol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"W547","DOI":"10.1093\/nar\/gkaf394","article-title":"The UniProt website API: Facilitating programmatic access to protein knowledge","volume":"53","author":"Ahmad","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"W318","DOI":"10.1093\/nar\/gkae270","article-title":"The structure assessment web server: For proteins, complexes and more","volume":"52","author":"Waterhouse","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"W194","DOI":"10.1093\/nar\/gkae415","article-title":"CASTpFold: Computed Atlas of Surface Topography of the universe of protein Folds","volume":"52","author":"Ye","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_87","unstructured":"Schr\u00f6dinger, L. (The PyMOL Molecular Graphics System, 2025). The PyMOL Molecular Graphics System, Version 3.0."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/12\/2140\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T15:13:17Z","timestamp":1781709197000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/12\/2140"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,17]]},"references-count":87,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["molecules31122140"],"URL":"https:\/\/doi.org\/10.3390\/molecules31122140","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,17]]}}}