{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T18:06:24Z","timestamp":1779818784174,"version":"3.53.1"},"reference-count":32,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Gansu Provincial Forestry and Grassland Science and Technology Project","award":["2022kj074"],"award-info":[{"award-number":["2022kj074"]}]},{"name":"Yunnan Plateau Characteristic Agriculture Science and Technology Program Project","award":["202502AE090016"],"award-info":[{"award-number":["202502AE090016"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    To explore the allelopathic response mechanism of\n                    <jats:italic>Elymus nutans<\/jats:italic>\n                    to the extracts of\n                    <jats:italic>Ligularia sagitta<\/jats:italic>\n                    , seed germination tests combined with integrated transcriptome and metabolome analyses were performed to systematically investigate the effects of the extracts at different concentrations on its germination characteristics and molecular metabolism. The results showed that the concentration range of 0.01\u20130.10\u2009mg\/mL was the sensitive interval for the allelopathic response of\n                    <jats:italic>Elymus nutans<\/jats:italic>\n                    to the extracts of\n                    <jats:italic>Ligularia sagitta<\/jats:italic>\n                    , and germination energy (GE) exhibited higher sensitivity to allelopathic stress than germination rate (GR). Transcriptome analysis yielded a total of 367463 Unigenes. In the comparison group of A and B,5617 differentially expressed genes (DEGs) were identified, including 3122 down-regulated genes and 2495 up-regulated genes. GO enrichment analysis revealed that these DEGs were mainly involved in biological processes such as biosynthesis and structural constituents of ribosomes. KEGG analysis indicated that 2683 DEGs were mapped to 133 pathways, of which 14 were significantly enriched, mainly covering pathways related to secondary metabolite biosynthesis, ribosome, and plant hormone signal transduction. Metabolome analysis identified 361 differential metabolites (DMs), which were annotated to 79 pathways with 29 significantly enriched ones. Integrated transcriptome and metabolome analysis revealed that DEMs and DMs were mainly enriched in two KEGG functional categories, namely Genetic Information Processing and Metabolism. Among these, the phenylpropanoid biosynthesis pathway was identified as the core secondary metabolic pathway in response to allelopathic stress. This pathway relies on a series of enzymatic reactions catalyzed by key genes including phenylalanine ammonia-lyase (\n                    <jats:italic>PAL<\/jats:italic>\n                    ), phenylalanine\/tyrosine ammonia-lyase (\n                    <jats:italic>PTAL<\/jats:italic>\n                    ), cinnamyl alcohol dehydrogenase (\n                    <jats:italic>CAD<\/jats:italic>\n                    ) and cinnamoyl-CoA reductase (\n                    <jats:italic>CCR<\/jats:italic>\n                    ), together with key metabolites such as p-Coumaric acid, Ferulic acid and Sinapyl alcohol, to produce metabolic products including lignin and flavonoids. This study provides a theoretical basis for revealing the molecular mechanism underlying the allelopathic response of\n                    <jats:italic>Elymus nutans<\/jats:italic>\n                    to the extracts of\n                    <jats:italic>Ligularia sagitta<\/jats:italic>\n                    , and also offers a scientific basis for the conservation and sustainable utilization of grassland ecosystems in alpine regions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0349098","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T17:40:20Z","timestamp":1779817220000},"page":"e0349098","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic and metabolomic analysis of allelopathic responses in Elymus nutans"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-2464-7515","authenticated-orcid":true,"given":"Huiyun","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingming","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianping","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijing","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3069-7681","authenticated-orcid":true,"given":"Yifu","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"issue":"1","key":"pone.0349098.ref001","first-page":"99","article-title":"Correlation analysis between seed yield and agronomic traits of Elymus nutans in Baqing","volume":"41","author":"JT Long","year":"2024","journal-title":"Pratacult Sci"},{"issue":"5","key":"pone.0349098.ref002","first-page":"899","article-title":"Insecticidal and antifungal activities of extracts from three Ligularia species","volume":"39","author":"J Li","year":"2022","journal-title":"Pratacult Sci"},{"issue":"04","key":"pone.0349098.ref003","first-page":"22","article-title":"Effects of temperature and mixed sowing ratio on population growth and interspecific competition of Onobrychis viciaefolia-Elymus nutans community","volume":"43","author":"WT Jing","year":"2021","journal-title":"Chin J Grassland"},{"issue":"05","key":"pone.0349098.ref004","first-page":"1454","article-title":"Effects of cross-sowing at different growth stages on Elymus nutans and Medicago sativa community","volume":"28","author":"ZY Yao","year":"2020","journal-title":"Acta Agrestia Sinica"},{"key":"pone.0349098.ref005","author":"SX Wang","year":"2024"},{"issue":"03","key":"pone.0349098.ref006","first-page":"108","article-title":"Research progress on the mechanism of action of plant allelochemicals","author":"HN Yang","year":"2022","journal-title":"Hunan Agric Sci"},{"key":"pone.0349098.ref007","author":"Y Gong","year":"2016"},{"issue":"8","key":"pone.0349098.ref008","article-title":"An investigation into the kinetics and mechanism of the removal of cyanobacteria by extract of Ephedra equisetina root","volume":"7","author":"R Yan","year":"2012","journal-title":"PLoS One"},{"key":"pone.0349098.ref009","doi-asserted-by":"crossref","first-page":"1609150","DOI":"10.3389\/fpls.2025.1609150","article-title":"The cabbage-leaf water extract can inhibit the germination and seedling growth of three receptor crops","volume":"16","author":"C Zhao","year":"2025","journal-title":"Front Plant Sci"},{"issue":"3","key":"pone.0349098.ref010","first-page":"1","article-title":"Research on the application of combined transcriptome and metabolome analysis in plants","volume":"42","author":"SY Xue","year":"2022","journal-title":"J Shanxi Agric Univ"},{"issue":"5","key":"pone.0349098.ref011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0232626","article-title":"Elicitation with Bacillus QV15 reveals a pivotal role of F3H on flavonoid metabolism improving adaptation to biotic stress in blackberry","volume":"15","author":"E Guti\u00e9rrez-Albanchez","year":"2020","journal-title":"PLoS One"},{"issue":"5","key":"pone.0349098.ref012","doi-asserted-by":"crossref","DOI":"10.1002\/cbdv.202402709","article-title":"Antioxidant effects of Moringa oleifera against abamectin-induced oxidative stress in the brain and erythrocytes of rats","volume":"22","author":"K Boudjema","year":"2025","journal-title":"Chem Biodivers"},{"key":"pone.0349098.ref013","unstructured":"Yao Y. The structure of the Brassica napus seed microbiota and the function of seed core microbes in enhancing growth and inducing disease resistance. Doctoral Dissertation of Huazhong Agricultural University; 2024. doi: 10.27158\/d.cnki.ghznu.2024.000084"},{"issue":"1","key":"pone.0349098.ref014","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"issue":"1","key":"pone.0349098.ref015","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pone.0349098.ref016","first-page":"1475","article-title":"Allelopathic effects of seedling-stage alfalfa (Medicago sativa) on seed germination and growth of Elymus nutans from different regions","volume":"39","author":"SHN Bao","year":"2019","journal-title":"Acta Ecol Sin"},{"issue":"4","key":"pone.0349098.ref017","first-page":"32","article-title":"Effects of aqueous extracts of Eupatorium adenophorum on seed germination and seedling growth of four crops","author":"GS Li","year":"2011","journal-title":"Modern Agric Sci Technol"},{"issue":"6","key":"pone.0349098.ref018","first-page":"907","article-title":"Allelopathic effects of Eupatorium adenophorum on rice seed germination","volume":"38","author":"ZF Zhao","year":"2023","journal-title":"J Yunnan Agric Univ (Nat Sci Ed)"},{"key":"pone.0349098.ref019","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.plaphy.2018.08.006","article-title":"Transcriptomic comparison of two barley genotypes differing in arsenic tolerance exposed to arsenate and phosphate treatments","volume":"130","author":"G Zvobgo","year":"2018","journal-title":"Plant Physiol Biochem"},{"key":"pone.0349098.ref020","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.bbaexp.2003.09.010","article-title":"Effects of additional sequences directly downstream from the AUG on the expression of GFP gene","volume":"1630","author":"K-N Zhao","year":"2003","journal-title":"Biochim Biophys Acta"},{"key":"pone.0349098.ref021","doi-asserted-by":"crossref","first-page":"877304","DOI":"10.3389\/fpls.2022.877304","article-title":"Environmental and genetic factors involved in plant protection-associated secondary metabolite biosynthesis pathways","volume":"13","author":"X Zhan","year":"2022","journal-title":"Front Plant Sci"},{"key":"pone.0349098.ref022","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.ijpharm.2014.05.049","article-title":"Enhancement of solubility, antioxidant ability and bioavailability of taxifolin nanoparticles by liquid antisolvent precipitation technique","volume":"471","author":"Y Zu","year":"2014","journal-title":"Int J Pharm"},{"issue":"4","key":"pone.0349098.ref023","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1007\/s10517-014-2584-z","article-title":"PI3K, MAPK EPK1\/2 and p38 are involved in the realization of growth potential of mesenchymal progenitor cells under the influence of basic fibroblast growth factor","volume":"157","author":"GN Zyuz\u2019kov","year":"2014","journal-title":"Bull Exp Biol Med"},{"issue":"21","key":"pone.0349098.ref024","doi-asserted-by":"crossref","first-page":"10568","DOI":"10.1073\/pnas.1900482116","article-title":"JASSY, a chloroplast outer membrane protein required for jasmonate biosynthesis","volume":"116","author":"L Guan","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"pone.0349098.ref025","first-page":"1021","article-title":"Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development","volume":"111","author":"C Wasternack","year":"2013","journal-title":"Ann Bot"},{"issue":"21","key":"pone.0349098.ref026","doi-asserted-by":"crossref","first-page":"7797","DOI":"10.1128\/AEM.05676-11","article-title":"Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity","volume":"77","author":"W-Q Zhuang","year":"2011","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"pone.0349098.ref027","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1534\/g3.116.036020","article-title":"Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation","volume":"7","author":"D Zhao","year":"2017","journal-title":"G3 (Bethesda)"},{"key":"pone.0349098.ref028","doi-asserted-by":"crossref","first-page":"110536","DOI":"10.1016\/j.plaphy.2025.110536","article-title":"ABA orchestrates molecular networks linking antioxidant defense, sugar metabolism and circadian clock for combined stress tolerance in Quinoa (Chenopodium quinoa Willd.)","volume":"229","author":"Q Lu","year":"2025","journal-title":"Plant Physiol Biochem"},{"issue":"5","key":"pone.0349098.ref029","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1111\/tpj.13730","article-title":"Multifaceted plant responses to circumvent Phe hyperaccumulation by downregulation of flux through the shikimate pathway and by vacuolar Phe sequestration","volume":"92","author":"JH Lynch","year":"2017","journal-title":"Plant J"},{"issue":"7","key":"pone.0349098.ref030","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0306340","article-title":"Optimization of salicylic acid concentrations for increasing antioxidant enzymes and bioactive compounds of Agastache rugosa in a plant factory","volume":"19","author":"V Phong Lam","year":"2024","journal-title":"PLoS One"},{"issue":"1","key":"pone.0349098.ref031","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1093\/mp\/ssq045","article-title":"The simultaneous repression of CCR and CAD, two enzymes of the lignin biosynthetic pathway, results in sterility and dwarfism in Arabidopsis thaliana","volume":"4","author":"J Th\u00e9venin","year":"2011","journal-title":"Mol Plant"},{"key":"pone.0349098.ref032","doi-asserted-by":"crossref","first-page":"140937","DOI":"10.1016\/j.foodchem.2024.140937","article-title":"Characterization of a longan pericarp browning related peroxidase with a focus on its role in proanthocyanidin and lignin polymerization","volume":"461","author":"J Wei","year":"2024","journal-title":"Food Chem"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0349098","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T17:40:30Z","timestamp":1779817230000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0349098"}},"subtitle":[],"editor":[{"given":"Chandran","family":"Janani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,5,26]]},"references-count":32,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0349098","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,26]]}}}