{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T16:28:06Z","timestamp":1790958486452,"version":"4.1.0"},"reference-count":48,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81473297"],"award-info":[{"award-number":["81473297"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["2014JM4136"],"award-info":[{"award-number":["2014JM4136"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007128","name":"Natural Science Foundation of Shaanxi Province","doi-asserted-by":"publisher","award":["81473297"],"award-info":[{"award-number":["81473297"]}],"id":[{"id":"10.13039\/501100007128","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007128","name":"Natural Science Foundation of Shaanxi Province","doi-asserted-by":"publisher","award":["2014JM4136"],"award-info":[{"award-number":["2014JM4136"]}],"id":[{"id":"10.13039\/501100007128","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Gentiana macrophylla Pall. (G. macrophylla)\u2014a member of the family Gentianaceae\u2014is a well-known traditional Chinese medical herb. Iridoids are the main active components of G. macrophylla, which has a wide range of pharmacological activities such as dispelling wind, eliminating dampness, clearing heat and asthenic fever, hepatoprotective and choleretic actions, and other medicinal effects. In this study, a total of 67,048 unigenes were obtained by transcriptomic sequencing analysis of G. macrophylla. A BLAST analysis showed that 48.21%, 33.66%, 46.32%, and 32.62% of unigenes were identified in the NR, Swiss-Prot, eggNOG, and KEGG databases, respectively. Twenty-five key enzymes were identified in the iridoid biosynthesis pathway. Most of the upregulated unigenes were enriched in flowers and leaves. The trustworthiness of the transcriptomic data was validated by real-time quantitative PCR (qRT-PCR). A total of 22 chemical constituents were identified by ultra-high performance liquid chromatography-quadrupole-electrostatic field Orbitrap mass spectrometry (UPLC-Q-Exactive MS), including 10 iridoids. A correlation analysis showed that the expression of 7-DLH and SLS was closely related to iridoids. The expression of 7-DLH and SLS was higher in flowers, indicating that flowers are important for iridoid biosynthesis in G. macrophylla.<\/jats:p>","DOI":"10.3390\/genes13122372","type":"journal-article","created":{"date-parts":[[2022,12,16]],"date-time":"2022-12-16T02:16:41Z","timestamp":1671157001000},"page":"2372","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["A Comparative Transcriptomic with UPLC-Q-Exactive MS Reveals Differences in Gene Expression and Components of Iridoid Biosynthesis in Various Parts of Gentiana macrophylla"],"prefix":"10.3390","volume":"13","author":[{"given":"Yuhang","family":"Kou","sequence":"first","affiliation":[{"name":"College of Life Sciences, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoying","family":"Yi","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuo","family":"Li","sequence":"additional","affiliation":[{"name":"Xi\u2019an Institute for Food and Drug Control, Xi\u2019an 710054, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Ai","sequence":"additional","affiliation":[{"name":"Xi\u2019an Institute for Food and Drug Control, Xi\u2019an 710054, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siting","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianliang","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Northwest University, Xi\u2019an 710069, China"},{"name":"Biomedicine Key Laboratory of Shaanxi Province, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"key":"ref_1","first-page":"3176","article-title":"Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix","volume":"41","author":"Lu","year":"2016","journal-title":"China J. Chin. Mater. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.jep.2010.07.051","article-title":"Identification of medicinal plants used as Tibetan traditional medicine Jie-Ji","volume":"132","author":"Zhao","year":"2010","journal-title":"J. Ethnopharmacol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1080\/14786411003745494","article-title":"Chemical constituents of Gentiana macrophylla Pall","volume":"24","author":"Jiang","year":"2010","journal-title":"Nat. Prod. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1002\/cbdv.201500333","article-title":"Phytochemistry and pharmacological activities of the genus Gentiana (Gentianaceae)","volume":"13","author":"Pan","year":"2016","journal-title":"Chem. Biodivers."},{"key":"ref_5","first-page":"3766","article-title":"Prediction of the ecological suitability of Gentiana macrophylla Pall. under scenarios of global climate change","volume":"39","author":"Tan","year":"2020","journal-title":"Chin. J. Ecol."},{"key":"ref_6","first-page":"63","article-title":"Biosynthesis and biological functions of terpenoids in plants","volume":"148","author":"Tholl","year":"2015","journal-title":"Adv. Biochem. Eng.\/Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4817","DOI":"10.1007\/s11033-014-3352-x","article-title":"An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-seq","volume":"41","author":"Hua","year":"2014","journal-title":"Mol. Biol. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e1364","DOI":"10.1002\/wrna.1364","article-title":"RNA-Seq methods for transcriptome analysis","volume":"8","author":"Hrdlickova","year":"2017","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1186\/s12864-019-6000-y","article-title":"Hybrid sequencing of the Gynostemma pentaphyllum transcriptome provides new insights into gypenoside biosynthesis","volume":"20","author":"Liang","year":"2019","journal-title":"BMC Genom."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1007\/s11033-020-05294-w","article-title":"Transcriptome analysis of terpenoid biosynthetic genes and simple sequence repeat marker screening in Eucommia ulmoides","volume":"47","author":"Jin","year":"2020","journal-title":"Mol. Biol. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Hou, D.Y., Shi, L.C., Yang, M.M., Li, J., Zhou, S., Zhang, H.X., and Xu, H.W. (2018). De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0192610"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s12864-019-5584-6","article-title":"In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species\u2019 adaptability to environmental cues","volume":"20","author":"Zhou","year":"2019","journal-title":"BMC Genom."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1002\/pca.2883","article-title":"Metabolomics analysis and biological investigation of three Malvaceae plants","volume":"31","author":"Abdelhafez","year":"2020","journal-title":"Phytochem. Anal."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"110748","DOI":"10.1016\/j.plantsci.2020.110748","article-title":"Transcriptome-based metabolic profiling of flavonoids in Agave lechuguilla waste biomass","volume":"305","author":"Morreeuw","year":"2021","journal-title":"Plant Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"661296","DOI":"10.3389\/fgene.2021.661296","article-title":"Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers","volume":"12","author":"Li","year":"2021","journal-title":"Front. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"9717","DOI":"10.1038\/s41598-021-88511-1","article-title":"Study on effects of sweating treatment and different drying methods on the quality of Gentianae macrophyllae Radix","volume":"11","author":"Chen","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Boratyn, G.M., Thierry-Mieg, J., Thierry-Mieg, D., Busby, B., and Madden, T.L. (2019). Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinform., 20.","DOI":"10.1186\/s12859-019-2996-x"},{"key":"ref_24","first-page":"138","article-title":"ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences","volume":"99","author":"Iseli","year":"1999","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"ref_25","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":"2002","journal-title":"Methods"},{"key":"ref_26","first-page":"3175","article-title":"Rapid analysis on chemical constituents from roots of Gentiana crasicaulis by ultra-high performance liquid chromatography coupled with hybrid quadrupole-orbitrap mass spectrometry","volume":"47","author":"Wang","year":"2010","journal-title":"Chin. Tradit. Herb. Drugs"},{"key":"ref_27","first-page":"96","article-title":"Rapid analysis of 4 chemical compositions in Gentiana macrophylla by UPLC-LTQ-Orbitrap-MS","volume":"18","author":"Zhang","year":"2020","journal-title":"Cent. South Pharm."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1007\/s11418-011-0560-8","article-title":"Qualitative and quantitative determination of ten iridoids and secoiridoids in Gentiana straminea Maxim. by LC-UV-ESI-MS","volume":"66","author":"Wei","year":"2012","journal-title":"J. Nat. Med."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1080\/19440049.2020.1778187","article-title":"Determination of 12 herbal compounds for estimating the presence of Angelica Gigas Root, Cornus Fruit, Licorice Root, Pueraria Root, and Schisandra Fruit in foods by LC-MS\/MS","volume":"37","author":"Ahn","year":"2020","journal-title":"Food Addit. Contam. Part A"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1271\/bbb.60059","article-title":"Novel secoiridoid glucosides in Olea europaea leaves suffering from boron deficiency","volume":"70","author":"Karioti","year":"2006","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"ref_31","first-page":"527","article-title":"Chemical Constituents of Gentiana Macrophylla Pall. From Shaanxi","volume":"1","author":"Chen","year":"2006","journal-title":"Nat. Prod. Commun."},{"key":"ref_32","first-page":"1214","article-title":"Study on the chemical constituents in roots of Gentiana dahurica","volume":"8","author":"Chen","year":"2011","journal-title":"J. Chin. Med. Mater."},{"key":"ref_33","first-page":"3811","article-title":"Chemical constituents of Swertia kouitchensis Franch","volume":"40","author":"He","year":"2015","journal-title":"China J. Chin. Mater. Med."},{"key":"ref_34","first-page":"417","article-title":"Chemical Constituents of Gentiana waltonii","volume":"6","author":"Duan","year":"2007","journal-title":"Chin. J. Nat. Med."},{"key":"ref_35","first-page":"2052","article-title":"Chemical constituents from flower of Gentiana tibetica","volume":"46","author":"Li","year":"2015","journal-title":"Chin. Tradit. Herb. Drugs"},{"key":"ref_36","first-page":"2328","article-title":"Application of metabolomics approach to study on chemical constituents in different parts of Gentiana crasicaulis based on UPLC-ESI-HRMSn","volume":"49","author":"Chen","year":"2018","journal-title":"Chin. Tradit. Herb. Drugs"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"3771","DOI":"10.1002\/asia.202001034","article-title":"Recent Advances in Iridoid Chemistry: Biosynthesis and Chemical Synthesis","volume":"15","author":"Kouda","year":"2020","journal-title":"Chem. Asian J."},{"key":"ref_38","first-page":"4704","article-title":"Transcriptome analysis and validation of key genes involved in biosynthesis of iridoids in Gentiana lhassica","volume":"46","author":"Kang","year":"2021","journal-title":"China J. Chin. Mater. Med."},{"key":"ref_39","first-page":"944","article-title":"Analysis of transcriptomes to explore genes contributing to iridoid biosynthesis in Gentiana waltonii and Gentiana robusta (Gentianaceae)","volume":"54","author":"Ni","year":"2019","journal-title":"Acta Pharm. Sin."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.plantsci.2012.12.008","article-title":"Post-translational events and modifications regulating plant enzymes involved in isoprenoid precursor biosynthesis","volume":"203\u2013204","author":"Hemmerlin","year":"2013","journal-title":"Plant Sci."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"dsac034","DOI":"10.1093\/dnares\/dsac034","article-title":"De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids","volume":"5","author":"Zhou","year":"2022","journal-title":"DNA Res."},{"key":"ref_42","first-page":"223","article-title":"The last gene involved in the MEP pathway of Artemisia annua: Cloning and characterization and functional identification","volume":"5","author":"Mei","year":"2011","journal-title":"J. Med. Plants Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1475","DOI":"10.1007\/s00299-009-0747-6","article-title":"Molecular characterization of the Oncidium orchid HDR gene encoding 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase, the last step of the methylerythritol phosphate pathway","volume":"28","author":"Huang","year":"2009","journal-title":"Plant Cell Rep."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1104\/pp.104.058735","article-title":"The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis","volume":"138","author":"Hsieh","year":"2005","journal-title":"Plant Physiol."},{"key":"ref_45","unstructured":"National Pharmacopoeia Committee (2020). Pharmacopoeia of Peoples Republic of China, Chemical Industry Press. Part 1."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Morreeuw, Z.P., Castillo-Quiroz, D., R\u00edos-Gonz\u00e1lez, L.J., Mart\u00ednez-Rinc\u00f3n, R., Estrada, N., Melchor-Mart\u00ednez, E.M., Iqbal, H.M.N., Parra-Sald\u00edvar, R., and Reyes, A.G. (2021). High Throughput Profiling of Flavonoid Abundance in Agave lechuguilla Residue-Valorizing under Explored Mexican Plant. Plants, 10.","DOI":"10.3390\/plants10040695"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.3389\/fpls.2020.01128","article-title":"Study on Quality Response to Environmental Factors and Geographical Traceability of Wild Gentiana rigescens Franch","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Plant Sci."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.copbio.2014.12.015","article-title":"Advances and current limitations in transcript-level control of gene expression","volume":"34","author":"Leavitt","year":"2015","journal-title":"Curr. Opin. Biotechnol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/12\/2372\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:42:16Z","timestamp":1760146936000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/12\/2372"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,15]]},"references-count":48,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["genes13122372"],"URL":"https:\/\/doi.org\/10.3390\/genes13122372","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,15]]}}}