{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T06:15:36Z","timestamp":1788156936914,"version":"build-2803163510"},"reference-count":34,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    <jats:italic>Paeonia lactiflora<\/jats:italic>\n                    Pall. (Chinese peony), a perennial plant indigenous to northeastern China, exhibits extensive flower-color variation, but the metabolite-gene relationships underlying anthocyanin accumulation remain incompletely understood. We integrated metabolomic and transcriptomic of petals from three cultivars with pink (cv. \u2018Exclusive Memory\u2019, PF), pale pink (cv. \u2018Salad\u2019, PPF), and white (cv. \u2018Duchess\u2019, WF) flowers. Metabolomic profiling detected 689 metabolites, including 169 flavonoids and six anthocyanins. Pairwise comparisons identified 153, 199, and 137 differentially accumulated metabolites in PF\n                    <jats:italic>vs.<\/jats:italic>\n                    PPF, PF\n                    <jats:italic>vs.<\/jats:italic>\n                    WF, and PPF\n                    <jats:italic>vs.<\/jats:italic>\n                    WF, respectively, with 27 metabolites shared among the three comparisons. The total anthocyanin signal in PF petals was 3.25-fold that in PPF petals and 60.37-fold that in WF petals. By contrast, the abundance of the individual compound cyanidin-3,5-\n                    <jats:italic>O<\/jats:italic>\n                    -diglucoside (cyanin) was 76.85-fold higher in PF than in WF and 23.10-fold higher in PPF than in WF, these values therefore describe compound-specific rather than total-anthocyanin differences. RNA-seq identified 6,777, 8,030, and 6,794 differentially expressed genes in the three pairwise comparisons, including 779 shared genes. Correlation analysis prioritized 21 flavonoid-pathway structural genes and 53 candidate transcription factors associated with anthocyanin abundance. Weighted gene co-expression network analysis identified a turquoise module positively associated with anthocyanins and a\n                    <jats:italic>DFR<\/jats:italic>\n                    -centered subnetwork containing 24 candidate transcription factors, including\n                    <jats:italic>MYB<\/jats:italic>\n                    and\n                    <jats:italic>bHLH<\/jats:italic>\n                    genes. qRT-PCR of 12 selected genes reproduced the RNA-seq expression trends. These results elucidate the metabolic basis of peony petal coloration and identify candidate regulatory networks and key genes potentially involved in anthocyanin biosynthesis, providing a foundation for future functional validation.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1907085","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:39:30Z","timestamp":1788154770000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated metabolome and transcriptome analysis reveals the potential mechanism of anthocyanin biosynthesis in Paeonia lactiflora Pall. flowers"],"prefix":"10.3389","volume":"17","author":[{"given":"Yang","family":"Cao","sequence":"first","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pin","family":"Lv","sequence":"additional","affiliation":[{"name":"Ethnic Medicine Innovation Center, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongchuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Agricultural and Animal Husbandry Technology Promotion Center","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Deng","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanxia","family":"Lv","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Agricultural and Animal Husbandry Technology Promotion Center","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuanling","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Xue","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Jia","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peifeng","family":"Xue","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaoqun","family":"Xu","sequence":"additional","affiliation":[{"name":"Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqin","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Inner Mongolia Medical University","place":["Hohhot, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2025.149762","article-title":"Integration of transcriptome and targeted metabolome reveals regulatory and structural genes involved in anthocyanin biosynthesis of four Ceiba speciosa germplasms","volume":"969","author":"Bai","year":"2025","journal-title":"Gene"},{"key":"B2","doi-asserted-by":"publisher","first-page":"2713","DOI":"10.1534\/g3.120.401451","article-title":"Alternative splicing regulation of anthocyanin biosynthesis in Camellia sinensis var. assamica unveiled by PacBio Iso-Seq","volume":"10","author":"Chen","year":"2020","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1093\/jxb\/erv549","article-title":"Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation","volume":"67","author":"Cho","year":"2016","journal-title":"J.\u00a0Exp. Bot."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.70434","article-title":"ODR1, the key seed dormancy and germination regulator, promotes seed proanthocyanidin biosynthesis via interaction with TTG1 and modulation of MBW complex activity","volume":"123","author":"Ding","year":"2025","journal-title":"Plant J."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2020.144700","article-title":"The identification of an R2R3-MYB transcription factor involved in regulating anthocyanin biosynthesis in Primulina swinglei flowers","volume":"752","author":"Feng","year":"2020","journal-title":"Gene"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.685136","article-title":"Unraveling the regulatory mechanism of color diversity in Camellia japonica petals by integrative transcriptome and metabolome analysis","volume":"12","author":"Fu","year":"2021","journal-title":"Front. Plant Sci."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0274013","article-title":"Widely targeted metabolomics reveals stamen petaloid tissue of Paeonia lactiflora Pall. as a potential pharmacological resource","volume":"17","author":"Hafeez","year":"2022","journal-title":"PloS One"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.933061","article-title":"BnaA03.ANS identified by metabolomics and RNA-seq plays an important role in pigmentation of red rapeseed (Brassica napus) petals","volume":"13","author":"Hao","year":"2022","journal-title":"Front. Plant Sci."},{"key":"B9","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1111\/nph.17139","article-title":"SPX4 interacts with both PHR1 and PAP1 to regulate critical steps in phosphorus-status-dependent anthocyanin biosynthesis","volume":"230","author":"He","year":"2020","journal-title":"New Phytol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1186\/s12864-015-1428-1","article-title":"Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum","volume":"16","author":"Hong","year":"2015","journal-title":"BMC Genomics"},{"key":"B11","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/s41438-018-0098-y","article-title":"SlMYB75, an MYB-type transcription factor, promotes anthocyanin accumulation and enhances volatile aroma production in tomato fruits","volume":"6","author":"Jian","year":"2019","journal-title":"Hortic. Res."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1093\/pcp\/pcm131","article-title":"Engineering of the rose flavonoid biosynthetic pathway successfully generated blue-hued flowers accumulating delphinidin","volume":"48","author":"Katsumoto","year":"2007","journal-title":"Plant Cell Physiol."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinf."},{"key":"B14","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1186\/s12870-022-03772-2","article-title":"PhUGT78A22, a novel glycosyltransferase in Paeonia \u2018He Xie\u2019, can catalyze the transfer of glucose to glucosylated anthocyanins during petal blotch formation","volume":"22","author":"Li","year":"2022","journal-title":"BMC Plant Biol."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03777-5","article-title":"Integrated transcriptomics and metabolomics analysis provides insight into anthocyanin biosynthesis for sepal color formation in Heptacodium miconioides","volume":"14","author":"Li","year":"2023","journal-title":"Front. Plant Sci."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10784-3","article-title":"Transcriptomic analysis unveils alterations in the genetic expression profile of tree peony (Paeonia suffruticosa Andrews) infected by Alternaria alternata","volume":"25","author":"Li","year":"2024","journal-title":"BMC Genomics"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21165680","article-title":"Cloning and functional characterization of dihydroflavonol 4-reductase gene involved in anthocyanin biosynthesis of chrysanthemum","volume":"21","author":"Lim","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1016\/j.ncrops.2025.100080","article-title":"Enhancements in cotton fiber length phenotyping and optimization of weighted gene co-expression network analysis through fiber elongation rate metrics","volume":"3","author":"Liu","year":"2026","journal-title":"New Crops"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1093\/pcp\/pcx076","article-title":"Advances in the MYB-bHLH-WD repeat pigment regulatory model: addition of a WRKY factor and co-option of an anthocyanin MYB for betalain regulation","volume":"58","author":"Lloyd","year":"2017","journal-title":"Plant Cell Physiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1186\/s12870-021-03063-w","article-title":"Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses","volume":"21","author":"Lu","year":"2021","journal-title":"BMC Plant Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1917","DOI":"10.1007\/s11032-014-0149-5","article-title":"Crossbreeding of transgenic flax plants overproducing flavonoids and glucosyltransferase results in progeny with improved antifungal and antioxidative properties","volume":"34","author":"Mierziak","year":"2014","journal-title":"Mol. Breed."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0072017","article-title":"Molecular cloning and characterization of three genes encoding dihydroflavonol-4-reductase from Ginkgo biloba in anthocyanin biosynthetic pathway","volume":"8","author":"Permyakov","year":"2013","journal-title":"PloS One"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1186\/s12870-025-07647-8","article-title":"Integrated metabolomic and transcriptomic profiling unveils anthocyanin regulation in chemically induced flower color variation of Impatiens hybrida \u2018Solarscape\u2019","volume":"25","author":"Tian","year":"2025","journal-title":"BMC Plant Biol."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3390\/molecules24224025","article-title":"Analysis of flavonoid metabolites in citrus peels (Citrus reticulata \u2018Dahongpao\u2019) using UPLC-ESI-MS\/MS","volume":"24","author":"Wang","year":"2019","journal-title":"Molecules"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1111\/ppl.70616","article-title":"Multiomics uncover the molecular basis and crosstalk between floral scent and color in Hedychium varieties","volume":"177","author":"Wang","year":"2025","journal-title":"Physiol. Plant"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1016\/j.ncrops.2024.100054","article-title":"Perspectives on developing natural colored cotton through carotenoid biofortification","volume":"2","author":"Wang","year":"2025","journal-title":"New Crops"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25074030","article-title":"Integrative metabolomic and transcriptomic analyses reveal the mechanism of petal blotch formation in Rosa persica","volume":"25","author":"Wang","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"B28","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.foodchem.2018.03.111","article-title":"A comparative metabolomics study of flavonoids in sweet potato with different flesh colors (Ipomoea batatas (L.) Lam)","volume":"260","author":"Wang","year":"2018","journal-title":"Food Chem."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.712038","article-title":"Integrated metabolomics and transcriptome analysis of flavonoid biosynthesis in safflower (Carthamus tinctorius L.) with different colors","volume":"12","author":"Wang","year":"2021","journal-title":"Front. Plant Sci."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2023.1172321","article-title":"Genome-wide identification and bioinformatics analysis of WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea (Rhododendron simsii)","volume":"14","author":"Wang","year":"2023","journal-title":"Front. Genet."},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03762-y","article-title":"Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals","volume":"22","author":"Xia","year":"2022","journal-title":"BMC Plant Biol."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-022-03800-9","article-title":"Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.)","volume":"22","author":"Xing","year":"2022","journal-title":"BMC Plant Biol."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2015.00500","article-title":"VIGS approach reveals the modulation of anthocyanin biosynthetic genes by CaMYB in chili pepper leaves","volume":"6","author":"Zhang","year":"2015","journal-title":"Front. Plant Sci."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2017.01545","article-title":"De novo assembly of the Camellia nitidissima transcriptome reveals key genes of flower pigment biosynthesis","volume":"8","author":"Zhou","year":"2017","journal-title":"Front. Plant Sci."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1907085\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:39:31Z","timestamp":1788154771000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1907085\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":34,"alternative-id":["10.3389\/fpls.2026.1907085"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2026.1907085","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,31]]},"article-number":"1907085"}}