{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T02:46:01Z","timestamp":1791859561192,"version":"4.3.4"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"General Project of Ningxia Natural Science Foundation","award":["2025AAC030235"],"award-info":[{"award-number":["2025AAC030235"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Plant Mol Biol"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1007\/s11103-026-01760-4","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:06:56Z","timestamp":1789034816000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pan-genome characterization of the maize 4CL gene family and its dynamic responses to abiotic stress"],"prefix":"10.1007","volume":"116","author":[{"given":"Jingbing","family":"Zhao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingshuang","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongnan","family":"Shao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"issue":"1","key":"1760_CR1","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","volume":"182","author":"M Alonge","year":"2020","unstructured":"Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D (2020) Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182(1):145\u2013161 e123","journal-title":"Cell"},{"key":"1760_CR2","doi-asserted-by":"publisher","first-page":"1571825","DOI":"10.3389\/fpls.2025.1571825","volume":"16","author":"OO Aluko","year":"2025","unstructured":"Aluko OO, Ninkuu V, Jianpei Y, Chen S, Zeng H, Dakurah FD (2025) Phenylpropanoids metabolism: Recent insight into stress tolerance and plant development cues. Front Plant Sci 16:1571825","journal-title":"Front Plant Sci"},{"issue":"1","key":"1760_CR3","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1146\/annurev.arplant.54.031902.134938","volume":"54","author":"W Boerjan","year":"2003","unstructured":"Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54(1):519\u2013546","journal-title":"Annu Rev Plant Biol"},{"key":"1760_CR4","doi-asserted-by":"publisher","first-page":"e17662","DOI":"10.1111\/mec.17662","volume":"34","author":"NS Catlin","year":"2025","unstructured":"Catlin NS, Agha HI, Platts AE, Munasinghe M, Hirsch CN, Josephs EB (2025) Structural variants contribute to phenotypic variation in maize. Mol Ecol 34:e17662","journal-title":"Mol Ecol"},{"key":"1760_CR5","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.copbio.2018.12.012","volume":"56","author":"I Cesarino","year":"2019","unstructured":"Cesarino I (2019) Structural features and regulation of lignin deposited upon biotic and abiotic stresses. Curr Opin Biotechnol 56:209\u2013214","journal-title":"Curr Opin Biotechnol"},{"issue":"11","key":"1760_CR6","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","volume":"16","author":"C Chen","year":"2023","unstructured":"Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y (2023) TBtools-II: a one for all, all for one bioinformatics platform for biological big-data mining. Mol Plant 16(11):1733\u20131742","journal-title":"Mol Plant"},{"key":"1760_CR7","doi-asserted-by":"publisher","first-page":"1116426","DOI":"10.3389\/fpls.2023.1116426","volume":"14","author":"SJ Choi","year":"2023","unstructured":"Choi SJ, Lee Z, Kim S, Jeong E, Shim JS (2023) Modulation of lignin biosynthesis for drought tolerance in plants. Front Plant Sci 14:1116426","journal-title":"Front Plant Sci"},{"issue":"12","key":"1760_CR8","doi-asserted-by":"publisher","first-page":"190215","DOI":"10.1098\/rsob.190215","volume":"9","author":"RA Dixon","year":"2019","unstructured":"Dixon RA, Barros J (2019) Lignin biosynthesis: old roads revisited and new roads explored. Open Biol 9(12):190215","journal-title":"Open Biol"},{"issue":"7","key":"1760_CR9","doi-asserted-by":"publisher","first-page":"1085","DOI":"10.2307\/3870059","volume":"7","author":"RA Dixon","year":"1995","unstructured":"Dixon RA, Paiva NL (1995) Stress-induced phenylpropanoid metabolism. Plant Cell 7(7):1085","journal-title":"Plant Cell"},{"issue":"1","key":"1760_CR10","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1111\/jipb.13054","volume":"63","author":"NQ Dong","year":"2021","unstructured":"Dong NQ, Lin HX (2021) Contribution of phenylpropanoid metabolism to plant development and plant\u2013environment interactions. J Integr Plant Biol 63(1):180\u2013209","journal-title":"J Integr Plant Biol"},{"issue":"1","key":"1760_CR11","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1046\/j.1365-313X.1999.00491.x","volume":"19","author":"J Ehlting","year":"1999","unstructured":"Ehlting J, B\u00fcttner D, Wang Q, Douglas CJ, Somssich IE, Kombrink E (1999) Three 4-coumarate: coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms. Plant J 19(1):9\u201320","journal-title":"Plant J"},{"issue":"3","key":"1760_CR12","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1111\/j.1469-8137.2009.02923.x","volume":"183","author":"LE Flagel","year":"2009","unstructured":"Flagel LE, Wendel JF (2009) Gene duplication and evolutionary novelty in plants. New Phytol 183(3):557\u2013564","journal-title":"New Phytol"},{"key":"1760_CR13","first-page":"e0152","volume":"9","author":"CM Fraser","year":"2011","unstructured":"Fraser CM, Chapple C (2011) The phenylpropanoid pathway in Arabidopsis. Arabidopsis Book\/Am Soc Plant Biol 9:e0152","journal-title":"Arabidopsis Book\/Am Soc Plant Biol"},{"issue":"2","key":"1760_CR14","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1104\/pp.111.178301","volume":"157","author":"J Gui","year":"2011","unstructured":"Gui J, Shen J, Li L (2011) Functional characterization of evolutionarily divergent 4-coumarate: coenzyme a ligases in rice. Plant Physiol 157(2):574\u2013586","journal-title":"Plant Physiol"},{"issue":"2","key":"1760_CR15","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1104\/pp.108.122457","volume":"148","author":"K Hanada","year":"2008","unstructured":"Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu S-H (2008) Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol 148(2):993\u20131003","journal-title":"Plant Physiol"},{"issue":"3","key":"1760_CR16","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/s41576-019-0180-9","volume":"21","author":"SS Ho","year":"2020","unstructured":"Ho SS, Urban AE, Mills RE (2020) Structural variation in the sequencing era. Nat Rev Genet 21(3):171\u2013189","journal-title":"Nat Rev Genet"},{"issue":"6555","key":"1760_CR17","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1126\/science.abg5289","volume":"373","author":"MB Hufford","year":"2021","unstructured":"Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y (2021) De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373(6555):655\u2013662","journal-title":"Science"},{"issue":"5","key":"1760_CR18","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1007\/s00425-018-2965-z","volume":"248","author":"SG Lavhale","year":"2018","unstructured":"Lavhale SG, Kalunke RM, Giri AP (2018) Structural, functional and evolutionary diversity of 4-coumarate-CoA ligase in plants. Planta 248(5):1063\u20131078","journal-title":"Planta"},{"issue":"4","key":"1760_CR19","first-page":"2409","volume":"169","author":"Y Li","year":"2015","unstructured":"Li Y, Kim JI, Pysh L, Chapple C (2015) Four isoforms of Arabidopsis 4-coumarate: CoA ligase have overlapping yet distinct roles in phenylpropanoid metabolism. Plant Physiol 169(4):2409\u20132421","journal-title":"Plant Physiol"},{"issue":"5494","key":"1760_CR20","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","volume":"290","author":"M Lynch","year":"2000","unstructured":"Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290(5494):1151\u20131155","journal-title":"Science"},{"key":"1760_CR21","doi-asserted-by":"crossref","unstructured":"Maren NA, Duduit JR, Huang D, Zhao F, Ranney TG, Liu W (2023) Stepwise optimization of real-time RT-PCR analysis. Plant genome engineering: methods and protocols. Springer, pp 317\u2013332","DOI":"10.1007\/978-1-0716-3131-7_20"},{"issue":"1","key":"1760_CR22","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268\u2013274","journal-title":"Mol Biol Evol"},{"issue":"4","key":"1760_CR23","doi-asserted-by":"publisher","first-page":"2294","DOI":"10.1104\/pp.16.00523","volume":"171","author":"N Panchy","year":"2016","unstructured":"Panchy N, Lehti-Shiu M, Shiu S-H (2016) Evolution of gene duplication in plants. Plant Physiol 171(4):2294\u20132316","journal-title":"Plant Physiol"},{"issue":"4","key":"1760_CR24","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nmeth.4197","volume":"14","author":"R Patro","year":"2017","unstructured":"Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C (2017) Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14(4):417\u2013419","journal-title":"Nat Methods"},{"issue":"2","key":"1760_CR25","first-page":"91","volume":"2","author":"J Raes","year":"2003","unstructured":"Raes J, Van de Peer Y (2003) Gene duplication, the evolution of novel gene functions, and detecting functional divergence. Appl Bioinf 2(2):91\u201310","journal-title":"Appl Bioinf"},{"issue":"5","key":"1760_CR26","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1111\/j.1365-313X.2012.04933.x","volume":"70","author":"A Saballos","year":"2012","unstructured":"Saballos A, Sattler SE, Sanchez E, Foster TP, Xin Z, Kang C, Pedersen JF, Vermerris W (2012) Brown midrib2 (Bmr2) encodes the major 4-coumarate: coenzyme A ligase involved in lignin biosynthesis in sorghum (Sorghum bicolor (L.) Moench). Plant J 70(5):818\u2013830","journal-title":"Plant J"},{"issue":"11","key":"1760_CR27","doi-asserted-by":"publisher","first-page":"e1000734","DOI":"10.1371\/journal.pgen.1000734","volume":"5","author":"NM Springer","year":"2009","unstructured":"Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence\/absence variation (PAV) in genome content. PLoS Genet 5(11):e1000734","journal-title":"PLoS Genet"},{"issue":"2","key":"1760_CR28","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.molp.2018.12.016","volume":"12","author":"Y Tao","year":"2019","unstructured":"Tao Y, Zhao X, Mace E, Henry R, Jordan D (2019) Exploring and exploiting pan-genomics for crop improvement. Mol Plant 12(2):156\u2013169","journal-title":"Mol Plant"},{"issue":"4","key":"1760_CR29","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1038\/nrg3185","volume":"13","author":"C Vogel","year":"2012","unstructured":"Vogel C, Marcotte EM (2012) Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet 13(4):227\u2013232","journal-title":"Nat Rev Genet"},{"issue":"1","key":"1760_CR30","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1093\/mp\/ssp106","volume":"3","author":"T Vogt","year":"2010","unstructured":"Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3(1):2\u201320","journal-title":"Mol Plant"},{"issue":"1","key":"1760_CR31","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/S1672-0229(10)60008-3","volume":"8","author":"D Wang","year":"2010","unstructured":"Wang D, Zhang Y, Zhang Z, Zhu J, Yu J (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinform 8(1):77\u201380","journal-title":"Genom Proteom Bioinform"},{"issue":"1","key":"1760_CR32","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1186\/s13068-019-1421-z","volume":"12","author":"W Xiong","year":"2019","unstructured":"Xiong W, Wu Z, Liu Y, Li Y, Su K, Bai Z, Guo S, Hu Z, Zhang Z, Bao Y (2019) Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants. Biotechnol Biofuels 12(1):82","journal-title":"Biotechnol Biofuels"},{"issue":"12","key":"1760_CR34","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/S0169-5347(00)01994-7","volume":"15","author":"Z Yang","year":"2000","unstructured":"Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15(12):496\u2013503","journal-title":"Trends Ecol Evol"},{"issue":"3","key":"1760_CR33","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1111\/pbi.12016","volume":"11","author":"F Yang","year":"2013","unstructured":"Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M (2013) Engineering secondary cell wall deposition in plants. Plant Biotechnol J 11(3):325\u2013335","journal-title":"Plant Biotechnol J"}],"container-title":["Plant Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11103-026-01760-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11103-026-01760-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11103-026-01760-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T02:03:54Z","timestamp":1791857034000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11103-026-01760-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,10]]},"references-count":34,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,10]]}},"alternative-id":["1760"],"URL":"https:\/\/doi.org\/10.1007\/s11103-026-01760-4","relation":{},"ISSN":["0167-4412","1573-5028"],"issn-type":[{"value":"0167-4412","type":"print"},{"value":"1573-5028","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,10]]},"assertion":[{"value":"13 April 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"96"}}