{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T18:05:35Z","timestamp":1784657135387,"version":"3.55.0"},"reference-count":103,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T00:00:00Z","timestamp":1784592000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    The CAD (Cinnamyl Alcohol Dehydrogenase) gene family is a key determinant for lignin biosynthesis in plants. In legumes, CAD enzymes are involved in the development of vascular tissues such as xylem and Casparian strip and they contribute to the production of antimicrobial and antifungal compounds. Thereby, it offers defense against pathogens and pests. Despite their biological significance, a comparative genome-wide analysis of the CAD gene family in\n                    <jats:italic>Medicago truncatula<\/jats:italic>\n                    and\n                    <jats:italic>Lotus japonicus<\/jats:italic>\n                    has not been explored. Therefore, we conducted a comparative genome-wide study to investigate the characteristics and potential role of CAD genes in these two model legume species. A total of 51 CAD genes were identified in\n                    <jats:italic>M. truncatula<\/jats:italic>\n                    (\n                    <jats:italic>MtCAD<\/jats:italic>\n                    ) and 35 in\n                    <jats:italic>L. japonicus<\/jats:italic>\n                    (\n                    <jats:italic>LjCAD<\/jats:italic>\n                    ). The CAD proteins are prominently characterized by ADH_N and ADH_zinc_N domains that were distributed in 8 and 6 chromosomes of\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and\n                    <jats:italic>LjCAD<\/jats:italic>\n                    , respectively. Structural organization and conserved motif analysis indicated notable similarities between MtCAD and LjCAD proteins. However, considering the ancestry and functionality and based on the evolutionary analysis,\n                    <jats:italic>LjCAD<\/jats:italic>\n                    showed more similarities with\n                    <jats:italic>Arabidopsis<\/jats:italic>\n                    than\n                    <jats:italic>MjCAD<\/jats:italic>\n                    . Gene duplication analysis identified twelve duplicated gene pairs in\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and eight in\n                    <jats:italic>LjCAD,<\/jats:italic>\n                    including both tandem and segmental duplication events\n                    <jats:italic>.<\/jats:italic>\n                    Most\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and\n                    <jats:italic>LjCAD<\/jats:italic>\n                    were found in the cytoplasm with some of the\n                    <jats:italic>cis<\/jats:italic>\n                    -acting regulatory elements associated with stress responses. Gene Ontology annotation suggested that most\n                    <jats:italic>MtCAD<\/jats:italic>\n                    genes were associated with biological processes whereas\n                    <jats:italic>LjCAD<\/jats:italic>\n                    genes are mainly enriched in molecular functions. Both\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and\n                    <jats:italic>LjCAD<\/jats:italic>\n                    showed potential roles in secondary metabolite production. Three substantial transcription factor families such as bZIP, C2H2, and ERF and several unique microRNAs were predicted to target\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and\n                    <jats:italic>LjCAD<\/jats:italic>\n                    in regulating their gene expression against certain abiotic stressors for instance cold, freezing, drought, and heat. The\n                    <jats:italic>MtCAD<\/jats:italic>\n                    and\n                    <jats:italic>LjCAD<\/jats:italic>\n                    expressed highly in stress-responsive tissues such as nodule, root, immature flower, seed, and leaf. Meanwhile, RNA-sequencing data further highlighted several potential stress-responsive genes. In\n                    <jats:italic>M. truncatula<\/jats:italic>\n                    , The\n                    <jats:italic>MtCAD1<\/jats:italic>\n                    ,\n                    <jats:italic>MtCAD3<\/jats:italic>\n                    ,\n                    <jats:italic>MtCAD9<\/jats:italic>\n                    ,\n                    <jats:italic>MtCAD15<\/jats:italic>\n                    ,\n                    <jats:italic>MtCAD23<\/jats:italic>\n                    ,\n                    <jats:italic>MtCAD27<\/jats:italic>\n                    , and\n                    <jats:italic>MtCAD47<\/jats:italic>\n                    exhibited higher expression under cold, drought, and freezing stress compared with control conditions. Whereas in\n                    <jats:italic>L. japonicus<\/jats:italic>\n                    ,\n                    <jats:italic>LjCAD6<\/jats:italic>\n                    ,\n                    <jats:italic>LjCAD8<\/jats:italic>\n                    , and\n                    <jats:italic>LjCAD11<\/jats:italic>\n                    showed higher expression under cold, drought, and heat stress. Thus, these genes may serve as promising candidates for improving abiotic stress tolerance and provide molecular insights into their functional roles for future crop improvement programs and experimental validation.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0353726","type":"journal-article","created":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T17:33:41Z","timestamp":1784655221000},"page":"e0353726","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative genome-wide analysis of CAD (Cinnamyl Alcohol Dehydrogenase) gene family in Medicago truncatula and Lotus japonicus and their expression profiles in response to various abiotic abiotic stresses"],"prefix":"10.1371","volume":"21","author":[{"given":"Mst. 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Res"},{"issue":"4","key":"pone.0353726.ref003","doi-asserted-by":"crossref","first-page":"312","DOI":"10.3390\/pathogens9040312","article-title":"Phenylpropanoid Pathway Engineering: An Emerging Approach towards Plant Defense","volume":"9","author":"V Yadav","year":"2020","journal-title":"Pathogens"},{"issue":"1","key":"pone.0353726.ref004","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1039\/D3NP00012E","article-title":"Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production","volume":"41","author":"Z Zhu","year":"2024","journal-title":"Nat Prod Rep"},{"key":"pone.0353726.ref005","doi-asserted-by":"crossref","first-page":"840397","DOI":"10.3389\/fpls.2022.840397","article-title":"Identification and Characterization of Cinnamyl Alcohol Dehydrogenase Encoding Genes Involved in Lignin Biosynthesis and Resistance to Verticillium dahliae in Upland Cotton (Gossypium hirsutum L.)","volume":"13","author":"H Li","year":"2022","journal-title":"Front Plant Sci"},{"key":"pone.0353726.ref006","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1023\/B:PHYT.0000047809.65444.a4","article-title":"Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids","volume":"3","author":"J Ralph","year":"2004","journal-title":"Phytochemistry Reviews"},{"issue":"9","key":"pone.0353726.ref007","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1093\/jxb\/erq093","article-title":"Phenotypic plasticity in cell walls of maize brown midrib mutants is limited by lignin composition","volume":"61","author":"W Vermerris","year":"2010","journal-title":"J Exp Bot"},{"issue":"10","key":"pone.0353726.ref008","doi-asserted-by":"crossref","first-page":"6652","DOI":"10.1007\/s00344-023-10926-z","article-title":"Lignin: the building block of defense responses to stress in plants","volume":"42","author":"S Yadav","year":"2023","journal-title":"J Plant Growth Regul"},{"issue":"7","key":"pone.0353726.ref009","first-page":"1444","article-title":"CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri)","volume":"10","author":"K Qi","year":"2021","journal-title":"Plants (Basel)"},{"issue":"9","key":"pone.0353726.ref010","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1039\/b601672c","article-title":"Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4","volume":"4","author":"B Youn","year":"2006","journal-title":"Org Biomol Chem"},{"issue":"3","key":"pone.0353726.ref011","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1111\/mpp.12755","article-title":"The cotton laccase gene GhLAC15 enhances Verticillium wilt resistance via an increase in defence-induced lignification and lignin components in the cell walls of plants","volume":"20","author":"Y Zhang","year":"2019","journal-title":"Mol Plant Pathol"},{"key":"pone.0353726.ref012","doi-asserted-by":"crossref","first-page":"358","DOI":"10.3389\/fpls.2014.00358","article-title":"The role of the secondary cell wall in plant resistance to pathogens","volume":"5","author":"E Miedes","year":"2014","journal-title":"Frontiers in Plant Science"},{"issue":"2","key":"pone.0353726.ref013","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1111\/pbi.14201","article-title":"The elicitor VP2 from Verticillium dahliae triggers defence response in cotton","volume":"22","author":"P Qiu","year":"2024","journal-title":"Plant Biotechnol J"},{"issue":"4","key":"pone.0353726.ref014","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1007\/s00299-021-02672-x","article-title":"GhMYB4 downregulates lignin biosynthesis and enhances cotton resistance to Verticillium dahliae","volume":"40","author":"S Xiao","year":"2021","journal-title":"Plant Cell Rep"},{"issue":"4","key":"pone.0353726.ref015","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1071\/FP07297","article-title":"Medicago truncatula as a model for understanding plant interactions with other organisms, plant development and stress biology: past, present and future","volume":"35","author":"RJ Rose","year":"2008","journal-title":"Funct Plant Biol"},{"issue":"4","key":"pone.0353726.ref016","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1111\/j.1365-313X.1992.00487.x","article-title":"Lotus japonicus, an autogamous, diploid legume species for classical and molecular genetics","volume":"2","author":"K Handberg","year":"1992","journal-title":"Plant J"},{"key":"pone.0353726.ref017","doi-asserted-by":"crossref","DOI":"10.1105\/tpc.002451","article-title":"Rhizobium nod factor perception and signalling","volume":"14","author":"R Geurts","year":"2002","journal-title":"Plant Cell"},{"issue":"4","key":"pone.0353726.ref018","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.pbi.2011.03.016","article-title":"Regulation of signal transduction and bacterial infection during root nodule symbiosis","volume":"14","author":"C Popp","year":"2011","journal-title":"Curr Opin Plant Biol"},{"issue":"1","key":"pone.0353726.ref019","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1186\/1471-2164-15-1160","article-title":"The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula","volume":"15","author":"ML Friesen","year":"2014","journal-title":"BMC Genomics"},{"issue":"6","key":"pone.0353726.ref020","first-page":"819","article-title":"Transcriptomic analysis of L. Japonicus symbiosis reveals new candidate genes for local and systemic regulation of nodule function","volume":"10","author":"CM P\u00e9rez-Delgado","year":"2020","journal-title":"J Exp Bot"},{"key":"pone.0353726.ref021","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"DM Goodstein","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pone.0353726.ref022","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaa937","article-title":"SMART: recent updates, new developments and status in 2020","volume":"49","author":"I Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pone.0353726.ref023","article-title":"CDD\/SPARCLE: the conserved domain database in 2020","volume":"48","author":"S Lu","year":"2020","journal-title":"Nucleic Acids Research"},{"key":"pone.0353726.ref024","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"A Bateman","year":"2004","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"pone.0353726.ref025","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"K Tamura","year":"2021","journal-title":"Molecular Biology and Evolution"},{"issue":"8","key":"pone.0353726.ref026","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: phylogenetic analysis by maximum likelihood","volume":"24","author":"Z Yang","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"22","key":"pone.0353726.ref027","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"JD Thompson","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"pone.0353726.ref028","article-title":"Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"J Xie","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"pone.0353726.ref029","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"TL Bailey","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"pone.0353726.ref030","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1093\/nar\/30.1.42","article-title":"The KEGG databases at GenomeNet","volume":"30","author":"M Kanehisa","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"pone.0353726.ref031","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/cr.2009.6","article-title":"DOG 1.0: illustrator of protein domain structures","volume":"19","author":"J Ren","year":"2009","journal-title":"Cell Res"},{"issue":"8","key":"pone.0353726.ref032","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1093\/bioinformatics\/btu817","article-title":"GSDS 2.0: an upgraded gene feature visualization server","volume":"31","author":"B Hu","year":"2015","journal-title":"Bioinformatics"},{"issue":"8","key":"pone.0353726.ref033","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data","volume":"13","author":"C Chen","year":"2020","journal-title":"Mol Plant"},{"issue":"5494","key":"pone.0353726.ref034","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The evolutionary fate and consequences of duplicate genes","volume":"290","author":"M Lynch","year":"2000","journal-title":"Science"},{"issue":"7","key":"pone.0353726.ref035","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Y Wang","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0353726.ref036","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s43897-021-00020-x","article-title":"MG2C: a user-friendly online tool for drawing genetic maps","volume":"1","author":"J Chao","year":"2021","journal-title":"Mol Hortic"},{"key":"pone.0353726.ref037","doi-asserted-by":"crossref","unstructured":"Horton P, Park K-J, Obayashi T, Nakai K. Protein subcellular localization prediction with WoLF PSORT. In: Proceedings of the 4th Asia-Pacific bioinformatics conference, 2006.","DOI":"10.1142\/9781860947292_0007"},{"issue":"1","key":"pone.0353726.ref038","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/nar\/27.1.295","article-title":"PlantCARE, a plant cis-acting regulatory element database","volume":"27","author":"S Rombauts","year":"1999","journal-title":"Nucleic Acids Research"},{"key":"pone.0353726.ref039","volume-title":"R language and environment for statistical computing","author":"RCJC Team","year":"2020"},{"key":"pone.0353726.ref040","article-title":"PlantRegMap: charting functional regulatory maps in plants","volume":"48","author":"F Tian","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"pone.0353726.ref041","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"D Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pone.0353726.ref042","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0294236","article-title":"SRplot: A free online platform for data visualization and graphing","volume":"18","author":"D Tang","year":"2023","journal-title":"PLoS One"},{"issue":"11","key":"pone.0353726.ref043","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"key":"pone.0353726.ref044","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: from microRNA sequences to function","volume":"47","author":"A Kozomara","year":"2019","journal-title":"Nucleic Acids Research"},{"key":"pone.0353726.ref045","article-title":"psRNATarget: a plant small RNA target analysis server (2017 release)","volume":"46","author":"X Dai","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"pone.0353726.ref046","first-page":"2364","article-title":"Genome-Wide Identification and Characterization of the GASA Gene Family in Medicago truncatula, and Expression Patterns under Abiotic Stress and Hormone Treatments","volume":"13","author":"C Gao","year":"2024","journal-title":"Plants (Basel)"},{"key":"pone.0353726.ref047","doi-asserted-by":"crossref","first-page":"39447","DOI":"10.1038\/srep39447","article-title":"Lotus Base: An integrated information portal for the model legume Lotus japonicus","volume":"6","author":"T Mun","year":"2016","journal-title":"Sci Rep"},{"issue":"8","key":"pone.0353726.ref048","first-page":"1151","article-title":"Comparative Genomics of Lotus japonicus Reveals Insights into Proanthocyanidin Accumulation and Abiotic Stress Response","volume":"13","author":"Z Sun","year":"2024","journal-title":"Plants (Basel)"},{"key":"pone.0353726.ref049","first-page":"1247","article-title":"Genome-Wide Analysis of the AP2\/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula","volume":"6","author":"Y Shu","year":"2016","journal-title":"Front Plant Sci"},{"issue":"15","key":"pone.0353726.ref050","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0353726.ref051","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1114s51","article-title":"Mapping RNA-seq Reads with STAR","volume":"51","author":"A Dobin","year":"2015","journal-title":"Curr Protoc Bioinformatics"},{"issue":"16","key":"pone.0353726.ref052","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pone.0353726.ref053","first-page":"1","article-title":"RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"B Li","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"pone.0353726.ref054","first-page":"603","article-title":"The cinnamyl alcohol dehydrogenase (CAD) gene family in flax (Linum usitatissimum L.): Insight from expression profiling of cads induced by elicitors in cultured flax cells","volume":"68","author":"HS Eom","year":"2016","journal-title":"AoB Plants"},{"issue":"1","key":"pone.0353726.ref055","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1186\/s12870-024-05716-y","article-title":"Genome-wide identification of alcohol dehydrogenase (ADH) gene family in oilseed rape (Brassica napus L.) and BnADH36 functional verification under salt stress","volume":"24","author":"H Zhang","year":"2024","journal-title":"BMC Plant Biol"},{"issue":"1","key":"pone.0353726.ref056","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12864-023-09813-4","article-title":"Genome-wide identification and expression analysis of the ADH gene family under diverse stresses in tobacco (Nicotiana tabacum L.)","volume":"25","author":"R Wang","year":"2024","journal-title":"BMC Genomics"},{"key":"pone.0353726.ref057","first-page":"1","article-title":"The emerging trends and prospects of DNA methylomics for abiotic stress tolerance in legumes","author":"S Yadav","year":"2025","journal-title":"J Biotechnol"},{"key":"pone.0353726.ref058","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1146\/annurev.bi.40.070171.003253","article-title":"Protein-protein interaction and enzymatic activity","volume":"40","author":"C Frieden","year":"1971","journal-title":"Annu Rev Biochem"},{"issue":"5","key":"pone.0353726.ref059","doi-asserted-by":"crossref","first-page":"339","DOI":"10.2174\/0929866526666190228144219","article-title":"Applicability of Instability Index for In vitro Protein Stability Prediction","volume":"26","author":"DG Gamage","year":"2019","journal-title":"Protein Pept Lett"},{"issue":"6","key":"pone.0353726.ref060","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1007\/s00239-023-10145-w","article-title":"Functional diversification and the plant secondary cell wall","volume":"91","author":"JB Colbert","year":"2023","journal-title":"J Mol Evol"},{"key":"pone.0353726.ref061","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.3389\/fpls.2018.01535","article-title":"Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants","volume":"9","author":"J Zhang","year":"2018","journal-title":"Front Plant Sci"},{"issue":"3","key":"pone.0353726.ref062","first-page":"121","article-title":"Differential strategies of the model legumes Lotus japonicus and Medicago truncatula in the adaptation to salt stress: Photosynthetic and nutritional responses","volume":"3","author":"M L\u00f3pez","year":"2008","journal-title":"AJoPP"},{"key":"pone.0353726.ref063","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1007\/s00239-010-9378-3","article-title":"Evolution of the cinnamyl\/sinapyl alcohol dehydrogenase (CAD\/SAD) gene family: the emergence of real lignin is associated with the origin of bona fide CAD","volume":"71","author":"DM Guo","year":"2010","journal-title":"Journal of Molecular Evolution"},{"issue":"8","key":"pone.0353726.ref064","first-page":"1151","article-title":"Comparative Genomics of Lotus japonicus Reveals Insights into Proanthocyanidin Accumulation and Abiotic Stress Response","volume":"13","author":"Z Sun","year":"2024","journal-title":"Plants (Basel)"},{"key":"pone.0353726.ref065","doi-asserted-by":"crossref","unstructured":"Horan K, Shelton CR, Girke TJ. Predicting conserved protein motifs with Sub-HMMs. 2010;11:1\u201315.","DOI":"10.1186\/1471-2105-11-205"},{"key":"pone.0353726.ref066","first-page":"161","article-title":"Protein structural motifs in prediction and design","volume":"44","author":"CO Mackenzie","year":"2017","journal-title":"J Coisb"},{"key":"pone.0353726.ref067","doi-asserted-by":"crossref","unstructured":"Wang R, Du C, Gu G, Zhang B, Lin X, Chen C. Genome-wide identification and expression analysis of the ADH gene family in tobacco (Nicotiana tabacum L.). 2023.","DOI":"10.21203\/rs.3.rs-3219543\/v1"},{"issue":"1","key":"pone.0353726.ref068","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1186\/s12864-024-10577-8","article-title":"Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L","volume":"25","author":"T Li","year":"2024","journal-title":"BMC Genomics"},{"issue":"7","key":"pone.0353726.ref069","doi-asserted-by":"crossref","first-page":"2251","DOI":"10.1093\/jxb\/erac431","article-title":"Alternative splicing in plants: current knowledge and future directions for assessing the biological relevance of splice variants","volume":"74","author":"RS Tognacca","year":"2023","journal-title":"J Exp Bot"},{"key":"pone.0353726.ref070","doi-asserted-by":"crossref","first-page":"714","DOI":"10.3389\/fpls.2017.00714","article-title":"Genome-Wide Identification of Sorghum bicolor Laccases Reveals Potential Targets for Lignin Modification","volume":"8","author":"J Wang","year":"2017","journal-title":"Front Plant Sci"},{"issue":"5875","key":"pone.0353726.ref071","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1126\/science.1153917","article-title":"Synteny and collinearity in plant genomes","volume":"320","author":"H Tang","year":"2008","journal-title":"Science"},{"issue":"1","key":"pone.0353726.ref072","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1111\/j.1600-0587.2012.07348.x","article-title":"Collinearity: a review of methods to deal with it and a simulation study evaluating their performance","volume":"36","author":"CF Dormann","year":"2013","journal-title":"Ecography"},{"issue":"5","key":"pone.0353726.ref073","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1007\/s00425-004-1385-4","article-title":"Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification","volume":"220","author":"CM Tobias","year":"2005","journal-title":"Planta"},{"issue":"6","key":"pone.0353726.ref074","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1073\/pnas.0307987100","article-title":"Functional reclassification of the putative cinnamyl alcohol dehydrogenase multigene family in Arabidopsis","volume":"101","author":"S-J Kim","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0353726.ref075","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1749-6632.2011.06384.x","article-title":"Genome and gene duplications and gene expression divergence: a view from plants","volume":"1256","author":"Y Wang","year":"2012","journal-title":"Ann N Y Acad Sci"},{"key":"pone.0353726.ref076","doi-asserted-by":"crossref","unstructured":"Staggemeier VG, Diniz-Filho JAF, Forest F, Lucas EJA. Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest. 2015;115(5):747\u201361.","DOI":"10.1093\/aob\/mcv005"},{"issue":"9","key":"pone.0353726.ref077","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1016\/S0168-9525(02)02722-1","article-title":"The Ka\/Ks ratio: diagnosing the form of sequence evolution","volume":"18","author":"LD Hurst","year":"2002","journal-title":"Trends Genet"},{"issue":"8","key":"pone.0353726.ref078","article-title":"The Ka \/Ks and \u03c0a \/\u03c0s Ratios under Different Models of Gametophytic and Sporophytic Selection","volume":"15","author":"L-L Li","year":"2023","journal-title":"Genome Biol Evol"},{"key":"pone.0353726.ref079","doi-asserted-by":"crossref","first-page":"220","DOI":"10.3389\/fpls.2013.00220","article-title":"Plant cell wall lignification and monolignol metabolism","volume":"4","author":"Y Wang","year":"2013","journal-title":"Front Plant Sci"},{"key":"pone.0353726.ref080","doi-asserted-by":"crossref","unstructured":"Jensen PE, Leister DJF. Chloroplast evolution, structure and functions. 2014;6:40.","DOI":"10.12703\/P6-40"},{"key":"pone.0353726.ref081","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.plantsci.2013.12.007","article-title":"Identification and validation of promoters and cis-acting regulatory elements","author":"CM Hernandez-Garcia","year":"2014","journal-title":"Plant Sci"},{"key":"pone.0353726.ref082","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.plgene.2017.07.003","article-title":"Abscisic acid: A key regulator of abiotic stress tolerance in plants","volume":"11","author":"NA Dar","year":"2017","journal-title":"Plant Gene"},{"key":"pone.0353726.ref083","doi-asserted-by":"crossref","first-page":"950064","DOI":"10.3389\/fpls.2022.950064","article-title":"Genome-Wide Identification and Functional Analysis of Polyamine Oxidase Genes in Maize Reveal Essential Roles in Abiotic Stress Tolerance","volume":"13","author":"Y Xi","year":"2022","journal-title":"Front Plant Sci"},{"issue":"1","key":"pone.0353726.ref084","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/s10265-024-01601-9","article-title":"Systematic characterization of cinnamyl alcohol dehydrogenase members revealed classification and function divergence in Haplomitrium mnioides","volume":"138","author":"L Wang","year":"2025","journal-title":"J Plant Res"},{"key":"pone.0353726.ref085","doi-asserted-by":"crossref","first-page":"704697","DOI":"10.3389\/fpls.2021.704697","article-title":"Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants","volume":"12","author":"T Yao","year":"2021","journal-title":"Front Plant Sci"},{"issue":"1","key":"pone.0353726.ref086","doi-asserted-by":"crossref","first-page":"8740","DOI":"10.1038\/s41598-019-45072-8","article-title":"Computational identification of protein-protein interactions in model plant proteomes","volume":"9","author":"Z Ding","year":"2019","journal-title":"Sci Rep"},{"issue":"1","key":"pone.0353726.ref087","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1093\/bib\/bbx123","article-title":"Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods","volume":"20","author":"S Yang","year":"2019","journal-title":"Brief Bioinform"},{"key":"pone.0353726.ref088","volume-title":"KEGG bioinformatics resource for plant genomics and metabolomics","author":"MJPBM Kanehisa","year":"2016"},{"key":"pone.0353726.ref089","first-page":"437","article-title":"KEGG bioinformatics resource for plant genomics research","volume":"2007","author":"A Masoudi-Nejad","journal-title":"J Plant Biol Methods"},{"issue":"1","key":"pone.0353726.ref090","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s13568-024-01678-4","article-title":"Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum","volume":"14","author":"AA Abulfaraj","year":"2024","journal-title":"AMB Express"},{"key":"pone.0353726.ref091","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/1471-2164-12-220","article-title":"Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways","volume":"12","author":"HMM Ibrahim","year":"2011","journal-title":"BMC Genomics"},{"issue":"6","key":"pone.0353726.ref092","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1111\/jipb.12043","article-title":"Genome-wide analysis of plant-specific Dof transcription factor family in tomato","volume":"55","author":"X Cai","year":"2013","journal-title":"J Integr Plant Biol"},{"issue":"1","key":"pone.0353726.ref093","first-page":"127","article-title":"Plant transcription factor studies","volume":"49","author":"C Schwechheimer","year":"1998","journal-title":"Aropb"},{"key":"pone.0353726.ref094","first-page":"1427","article-title":"Regulation of lignin biosynthesis and its role in growth-defense tradeoffs","volume":"9","author":"M Xie","year":"2018","journal-title":"Fips"},{"issue":"7","key":"pone.0353726.ref095","doi-asserted-by":"crossref","first-page":"1915590","DOI":"10.1080\/15592324.2021.1915590","article-title":"MicroRNAs Roles in Plants Secondary Metabolism","volume":"16","author":"M Owusu Adjei","year":"2021","journal-title":"Plant Signal Behav"},{"issue":"11","key":"pone.0353726.ref096","doi-asserted-by":"crossref","first-page":"8141","DOI":"10.1111\/pce.70106","article-title":"Flavonoid\u2010lignin crosstalk: engineering metabolic flux for optimised plant growth and stress resilience","volume":"48","author":"J Yang","year":"2025","journal-title":"Cell Environment"},{"key":"pone.0353726.ref097","doi-asserted-by":"crossref","first-page":"102241","DOI":"10.1016\/j.pbi.2022.102241","article-title":"Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?","volume":"68","author":"AE Yaschenko","year":"2022","journal-title":"Curr Opin Plant Biol"},{"key":"pone.0353726.ref098","doi-asserted-by":"crossref","unstructured":"Jopcik M, Bauer M, Moravcikova J, Boszoradova E, Matusikova I, Libantova JJPC, et al. Plant tissue-specific promoters can drive gene expression in Escherichia coli. 2013;113:387\u201396.","DOI":"10.1007\/s11240-012-0278-7"},{"issue":"1","key":"pone.0353726.ref099","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/nrm.2015.6","article-title":"Plant vascular development: from early specification to differentiation","volume":"17","author":"B De Rybel","year":"2016","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pone.0353726.ref100","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1471-2229-9-26","article-title":"The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression","volume":"9","author":"A Barakat","year":"2009","journal-title":"BMC Plant Biol"},{"key":"pone.0353726.ref101","doi-asserted-by":"crossref","first-page":"139979","DOI":"10.1016\/j.ijbiomac.2025.139979","article-title":"The CaCAD1-CaPOA1 module positively regulates pepper resistance to cold stress by increasing lignin accumulation","volume":"290","author":"J Xiao","year":"2025","journal-title":"Int J Biol Macromol"},{"issue":"1","key":"pone.0353726.ref102","article-title":"Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems","volume":"21","author":"W Liu","year":"2021","journal-title":"BMC Plant Biol"},{"issue":"7","key":"pone.0353726.ref103","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.3390\/f14071465","article-title":"Transcriptomic Response to Drought Stress in Populus davidiana Dode","volume":"14","author":"M Yang","year":"2023","journal-title":"Forests"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0353726","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T17:33:57Z","timestamp":1784655237000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0353726"}},"subtitle":[],"editor":[{"given":"Mojtaba","family":"Kordrostami","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,21]]},"references-count":103,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0353726","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,21]]}}}