{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T11:01:53Z","timestamp":1789642913711,"version":"4.0.0"},"reference-count":83,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670335"],"award-info":[{"award-number":["31670335"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Plant Cell Rep"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1007\/s00299-026-03948-w","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T09:40:50Z","timestamp":1787910050000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Complete telomere-to-telomere genome assembly of Guazuma ulmifolia uncovers evolutionary mechanisms, drought adaptation, and flavonoid biosynthesis"],"prefix":"10.1007","volume":"45","author":[{"given":"Tashi","family":"Dorjee","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yican","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Richardson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3600-4970","authenticated-orcid":false,"given":"Fei","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"key":"3948_CR1","doi-asserted-by":"publisher","first-page":"123","DOI":"10.3329\/bjpt.v31i1.74393","volume":"31","author":"SS Ahmed","year":"2024","unstructured":"Ahmed SS, Rahman MO (2024) Systematics and morphometrics of the subfamily Byttnerioideae Burnett in Bangladesh. Bangladesh J Plant Taxon 31:123\u2013140","journal-title":"Bangladesh J Plant Taxon"},{"key":"3948_CR2","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.2307\/2656928","volume":"86","author":"WS Alverson","year":"1999","unstructured":"Alverson WS, Whitlock BA, Nyffeler R, Bayer C, Baum DA (1999) Phylogeny of the core Malvales: evidence from ndhF sequence data. Am J Bot 86:1474\u20131486","journal-title":"Am J Bot"},{"key":"3948_CR3","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/ng.736","volume":"43","author":"X Argout","year":"2011","unstructured":"Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN et al (2011) The genome of Theobroma cacao. Nat Genet 43:101\u2013108","journal-title":"Nat Genet"},{"key":"3948_CR4","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1038\/nature22380","volume":"546","author":"H Badouin","year":"2017","unstructured":"Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE, Cottret L, Lelandais-Bri\u00e8re C, Owens GL, Carr\u00e8re S, Mayjonade B et al (2017) The sunflower genome provides insights into oil metabolism, flowering and asterid evolution. Nature 546:148\u2013152","journal-title":"Nature"},{"key":"3948_CR5","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1093\/nar\/28.1.45","volume":"28","author":"A Bairoch","year":"2000","unstructured":"Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45\u201348","journal-title":"Nucleic Acids Res"},{"key":"3948_CR6","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573\u2013580","journal-title":"Nucleic Acids Res"},{"key":"3948_CR7","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter M-C, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O\u2019Donovan C, Phan I (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365\u2013370","journal-title":"Nucleic Acids Res"},{"key":"3948_CR8","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1016\/j.ympev.2007.06.012","volume":"44","author":"JW Borrone","year":"2007","unstructured":"Borrone JW, Meerow AW, Kuhn DN, Whitlock BA, Schnell RJ (2007) The potential of the WRKY gene family for phylogenetic reconstruction: an example from the Malvaceae. Mol Phylogenet Evol 44:1141\u20131154","journal-title":"Mol Phylogenet Evol"},{"key":"3948_CR9","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1111\/jse.13045","volume":"62","author":"AM Bossa\u2010Castro","year":"2024","unstructured":"Bossa\u2010Castro AM, Colli\u2010Silva M, Pirani JR, Whitlock BA, Morales Mancera LT, Contreras\u2010Ortiz N, Cepeda\u2010Hern\u00e1ndez ML, Di Palma F, Vives M, Richardson JE (2024) A phylogenetic framework to study desirable traits in the wild relatives of Theobroma cacao (Malvaceae). J Syst Evol 62:963\u2013978","journal-title":"J Syst Evol"},{"key":"3948_CR10","first-page":"4.10.1","volume":"25","author":"N Chen","year":"2004","unstructured":"Chen N (2004) Using repeat masker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics 25:4.10.1-4.10.14","journal-title":"Curr Protoc Bioinformatics"},{"key":"3948_CR11","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2022.100469","volume":"4","author":"Y Chen","year":"2023","unstructured":"Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M (2023) A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. Plant Commun 4:100469","journal-title":"Plant Commun"},{"key":"3948_CR12","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","volume":"18","author":"H Cheng","year":"2021","unstructured":"Cheng H, Concepcion GT, Feng X, Zhang H, Li H (2021) Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18:170\u2013175","journal-title":"Nat Methods"},{"key":"3948_CR13","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1007\/s12228-024-09783-1","volume":"76","author":"M Colli-Silva","year":"2024","unstructured":"Colli-Silva M, Richardson JE, Bossa-Castro AM, Pirani JR (2024a) Phylogenetic evidence reshapes the taxonomy of Cacao and its allies (Theobroma and Herrania; Malvaceae, Byttnerioideae). Brittonia 76:53\u201361","journal-title":"Brittonia"},{"key":"3948_CR14","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1007\/s12225-024-10171-x","volume":"79","author":"M Colli-Silva","year":"2024","unstructured":"Colli-Silva M, Richardson JE, Michelangeli FA, Pirani JR (2024b) Expanding the cacao group: three new species of Theobroma sect. Herrania (Malvaceae: Byttnerioideae) from the Western Amazon Basin. Kew Bull 79:571\u2013582","journal-title":"Kew Bull"},{"key":"3948_CR15","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaa185","volume":"22","author":"MHP da Cruz","year":"2021","unstructured":"da Cruz MHP, Domingues DS, Saito PTM, Paschoal AR, Bugatti PH (2021) TERL: classification of transposable elements by convolutional neural networks. Brief Bioinform 22:bbaa185","journal-title":"Brief Bioinform"},{"key":"3948_CR16","volume":"10","author":"G Das","year":"2021","unstructured":"Das G, Shin H-S, Ningthoujam SS, Talukdar AD, Upadhyaya H, Tundis R, Das SK, Patra JK (2021) Systematics, phytochemistry, biological activities and health promoting effects of the plants from the subfamily Bombacoideae (family Malvaceae). Plants (Basel) 10:651","journal-title":"Plants (Basel)"},{"key":"3948_CR17","first-page":"785","volume":"47","author":"JC de Ara\u00fajo Neto","year":"1999","unstructured":"de Ara\u00fajo Neto JC, Bergemann de Aguiar I (1999) Desarrollo ontog\u00e9nico de pl\u00e1ntulas de Guazuma ulmifolia (Sterculiaceae). Rev Biol Trop 47:785\u2013790","journal-title":"Rev Biol Trop"},{"key":"3948_CR18","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1007\/s11627-022-10275-8","volume":"58","author":"M de Jesus Santana","year":"2022","unstructured":"de Jesus Santana M, Barbosa-J\u00fanior SM, Dias LLL, Silva LAS, da Silva GZ, Fortini EA, Batista DS, Otoni WC, da Costa Netto AP, Rocha DI (2022) A novel in vitro propagation system for West Indian elm [Guazuma ulmifolia Lam. (Malvaceae)]: a valuable medicinal woody species. In Vitro Cell Dev Biol-Plant 58:865\u2013875","journal-title":"In Vitro Cell Dev Biol-Plant"},{"key":"3948_CR19","doi-asserted-by":"publisher","DOI":"10.1016\/j.jep.2021.114363","volume":"279","author":"LF De Lima","year":"2021","unstructured":"De Lima LF, de Oliveira JO, Carneiro JNP, Lima CNF, Coutinho HDM, Morais-Braga MFB (2021) Ethnobotanical and antimicrobial activities of the Gossypium (Cotton) genus: a review. J Ethnopharmacol 279:114363","journal-title":"J Ethnopharmacol"},{"key":"3948_CR20","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/B978-0-12-803138-4.00010-1","volume-title":"Exotic fruits","author":"PA De Souza","year":"2018","unstructured":"De Souza PA, Moreira LF, Sarmento DH, da Costa FB (2018) Cacao\u2014Theobroma cacao. Exotic fruits. Elsevier, pp 69\u201376"},{"key":"3948_CR21","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1111\/pce.13207","volume":"41","author":"OP Dhankher","year":"2018","unstructured":"Dhankher OP, Foyer CH (2018) Climate resilient crops for improving global food security and safety. Plant Cell Environ 41:877\u2013884","journal-title":"Plant Cell Environ"},{"key":"3948_CR22","doi-asserted-by":"publisher","DOI":"10.1155\/2018\/2935051","volume":"2018","author":"JM Dos Santos","year":"2018","unstructured":"Dos Santos JM, Alfredo TM, Antunes K\u00c1, da Cunha JdSM, Costa EMA, Lima ES, Silva DB, Carollo CA, Schmitz WO, Boleti APdA (2018) Guazuma ulmifolia Lam. decreases oxidative stress in blood cells and prevents doxorubicin\u2010induced cardiotoxicity. Oxid Med Cell Longev 2018:2935051","journal-title":"Oxid Med Cell Longev"},{"key":"3948_CR23","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238","journal-title":"Genome Biol"},{"key":"3948_CR24","doi-asserted-by":"publisher","first-page":"9451","DOI":"10.1073\/pnas.1921046117","volume":"117","author":"JM Flynn","year":"2020","unstructured":"Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 117:9451\u20139457","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3948_CR25","unstructured":"Francis JK 1991. Guazuma ulmifolia Lam. Gu\u00e1cima. Sterculiaceae. Chocolate family. USDA Forest Service, Southern Forest Experiment Station, Institute of Tropical Forestry, 5 p. (SO-ITF-SM 47)."},{"key":"3948_CR26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200454","volume":"13","author":"L Gateau-Rey","year":"2018","unstructured":"Gateau-Rey L, Tanner EVJ, Rapidel B, Marelli JP, Royaert S (2018) Climate change could threaten cocoa production: effects of 2015-16 El Ni\u00f1o-related drought on cocoa agroforests in Bahia, Brazil. PLoS ONE 13:e0200454","journal-title":"PLoS ONE"},{"key":"3948_CR27","doi-asserted-by":"publisher","first-page":"41","DOI":"10.15648\/invefor.v4i1.4133","volume":"4","author":"MS Guti\u00e9rrez","year":"2024","unstructured":"Guti\u00e9rrez MS, Ram\u00edrez JA, Romero OIC (2024) Actividades biol\u00f3gicas de Guazuma ulmifolia: una revisi\u00f3n. Investigaci\u00f3n y Acci\u00f3n 4:41\u201357","journal-title":"Investigaci\u00f3n y Acci\u00f3n"},{"key":"3948_CR28","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","volume":"9","author":"BJ Haas","year":"2008","unstructured":"Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Robin CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9:R7","journal-title":"Genome Biol"},{"key":"3948_CR29","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2019.106606","volume":"140","author":"R Hern\u00e1ndez-Guti\u00e9rrez","year":"2019","unstructured":"Hern\u00e1ndez-Guti\u00e9rrez R, Magall\u00f3n S (2019) The timing of Malvales evolution: incorporating its extensive fossil record to inform about lineage diversification. Mol Phylogenet Evol 140:106606","journal-title":"Mol Phylogenet Evol"},{"key":"3948_CR30","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1055\/s-2006-958057","volume":"61","author":"M H\u00f6r","year":"1995","unstructured":"H\u00f6r M, Rimpler H, Heinrich M (1995) Inhibition of intestinal chloride secretion by proanthocyanidins from Guazuma ulmifolia. Planta Med 61:208\u2013212","journal-title":"Planta Med"},{"key":"3948_CR31","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1038\/s41588-019-0371-5","volume":"51","author":"Y Hu","year":"2019","unstructured":"Hu Y, Chen J, Fang L, Zhang Z, Ma W, Niu Y, Ju L, Deng J, Zhao T, Lian J et al (2019) Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet 51:739\u2013748","journal-title":"Nat Genet"},{"key":"3948_CR32","first-page":"87","volume":"14","author":"ZM Ibrahim","year":"2018","unstructured":"Ibrahim ZM, Hassan SA, El-Azab HM, Badawi A (2018) Cladistic analysis of some taxa in Malvaceae s.l. \u201cCore Malvales\u201d based on anatomical characteristics. Egypt J Exp Biol (Botany) 14:87\u2013105","journal-title":"Egypt J Exp Biol (Botany)"},{"key":"3948_CR33","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","volume":"45","author":"M Kanehisa","year":"2017","unstructured":"Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353\u2013D361","journal-title":"Nucleic Acids Res"},{"key":"3948_CR34","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772\u2013780","journal-title":"Mol Biol Evol"},{"key":"3948_CR35","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1007\/978-1-4939-9173-0_9","volume":"1962","author":"J Keilwagen","year":"2019","unstructured":"Keilwagen J, Hartung F, Grau J (2019) GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data. Methods Mol Biol 1962:161\u2013177","journal-title":"Methods Mol Biol"},{"key":"3948_CR36","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/B978-0-12-803138-4.00022-8","volume":"1","author":"S Ketsa","year":"2018","unstructured":"Ketsa S (2018) Durian\u2014Durio zibethinus. Exotic Fruits 1:169\u2013180","journal-title":"Exotic Fruits"},{"key":"3948_CR37","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37:907\u2013915","journal-title":"Nat Biotechnol"},{"key":"3948_CR38","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/1471-2105-5-59","volume":"5","author":"I Korf","year":"2004","unstructured":"Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59","journal-title":"BMC Bioinformatics"},{"key":"3948_CR39","first-page":"205","volume":"7","author":"NS Kumar","year":"2019","unstructured":"Kumar NS, Gurunani SG (2019) Guazuma ulmifolia LAM: A review for future view. J Med Plants Stud 7:205\u2013210","journal-title":"J Med Plants Stud"},{"key":"3948_CR40","doi-asserted-by":"publisher","first-page":"87","DOI":"10.5808\/GI.2014.12.3.87","volume":"12","author":"S-I Lee","year":"2014","unstructured":"Lee S-I, Kim N-S (2014) Transposable elements and genome size variations in plants. Genomics Inform 12:87\u201397","journal-title":"Genomics Inform"},{"key":"3948_CR41","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/ng.2987","volume":"46","author":"F Li","year":"2014","unstructured":"Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, Li Q, Ma Z, Lu C, Zou C et al (2014) Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 46:567\u2013572","journal-title":"Nat Genet"},{"key":"3948_CR42","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhad127","volume":"10","author":"Y Lin","year":"2023","unstructured":"Lin Y, Ye C, Li X, Chen Q, Wu Y, Zhang F, Pan R, Zhang S, Chen S, Wang X et al (2023) quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic Res 10:uhad127","journal-title":"Hortic Res"},{"key":"3948_CR43","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1590\/S0103-50532009000600016","volume":"20","author":"GC Lopes","year":"2009","unstructured":"Lopes GC, Rocha JC, Almeida GCd, de Mello JC (2009) Condensed tannins from the bark of Guazuma ulmifolia Lam. (Sterculiaceae). J Braz Chem Soc 20:1103\u20131109","journal-title":"J Braz Chem Soc"},{"key":"3948_CR44","doi-asserted-by":"publisher","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","volume":"20","author":"WH Majoros","year":"2004","unstructured":"Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878\u20132879","journal-title":"Bioinformatics"},{"key":"3948_CR45","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.phytochem.2012.10.011","volume":"86","author":"M Maldini","year":"2013","unstructured":"Maldini M, Di Micco S, Montoro P, Darra E, Mariotto S, Bifulco G, Pizza C, Piacente S (2013) Flavanocoumarins from Guazuma ulmifolia bark and evaluation of their affinity for STAT1. Phytochemistry 86:64\u201371","journal-title":"Phytochemistry"},{"key":"3948_CR46","doi-asserted-by":"publisher","first-page":"5516","DOI":"10.1093\/bioinformatics\/btaa1022","volume":"36","author":"FK Mendes","year":"2020","unstructured":"Mendes FK, Vanderpool D, Fulton B, Hahn MW (2020) CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36:5516\u20135518","journal-title":"Bioinformatics"},{"key":"3948_CR47","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530\u20131534","journal-title":"Mol Biol Evol"},{"key":"3948_CR48","doi-asserted-by":"publisher","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","volume":"49","author":"J Mistry","year":"2021","unstructured":"Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer EL, Tosatto SC, Paladin L, Raj S, Richardson LJ et al (2021) Pfam: the protein families database in 2021. Nucleic Acids Res 49:D412\u2013D419","journal-title":"Nucleic Acids Res"},{"key":"3948_CR49","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.sajb.2016.08.003","volume":"110","author":"S Morais","year":"2017","unstructured":"Morais S, Calixto-J\u00fanior J, Ribeiro L, Sousa H, Silva A, Figueiredo F, Matias E, Boligon A, Athayde M, Morais-Braga M et al (2017) Phenolic composition and antioxidant, anticholinesterase and antibiotic-modulating antifungal activities of Guazuma ulmifolia Lam. (Malvaceae) ethanol extract. S Afr J Bot 110:251\u2013257","journal-title":"S Afr J Bot"},{"key":"3948_CR50","doi-asserted-by":"publisher","first-page":"1750","DOI":"10.1002\/csc2.20959","volume":"63","author":"HE Nieves\u2010Ordu\u00f1a","year":"2023","unstructured":"Nieves\u2010Ordu\u00f1a HE, Krutovsky KV, Gailing O (2023) Geographic distribution, conservation, and genomic resources of cacao Theobroma cacao L. Crop Sci 63:1750\u20131778","journal-title":"Crop Sci"},{"key":"3948_CR51","doi-asserted-by":"publisher","first-page":"1886","DOI":"10.1093\/gbe\/evt141","volume":"5","author":"KR Oliver","year":"2013","unstructured":"Oliver KR, McComb JA, Greene WK (2013) Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 5:1886\u20131901","journal-title":"Genome Biol Evol"},{"key":"3948_CR52","doi-asserted-by":"publisher","first-page":"151","DOI":"10.35516\/jjps.v17i1.1171","volume":"17","author":"E Puspitasari","year":"2024","unstructured":"Puspitasari E, Triatmoko B, Dianasari D, Muslichah S, Nugraha AS (2024) Assessment of extraction methods effects on the biological activities (antioxidant and antiamylase) and chemistry (total phenolics and flavonoids) of Guazuma ulmifolia leaves. Jordan J Pharm Sci 17:151\u2013162","journal-title":"Jordan J Pharm Sci"},{"key":"3948_CR53","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s13059-019-1650-2","volume":"20","author":"X Qiao","year":"2019","unstructured":"Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH (2019) Gene duplication and evolution in recurring polyploidization\u2013diploidization cycles in plants. Genome Biol 20:38","journal-title":"Genome Biol"},{"key":"3948_CR54","doi-asserted-by":"publisher","first-page":"171","DOI":"10.22146\/ijp.598","volume":"31","author":"M Rafi","year":"2020","unstructured":"Rafi M, Meitary N, Septaningsih DA, Bintang M (2020) Phytochemical profile and antioxidant activity of Guazuma ulmifolia leaves extracts using different solvent extraction. Indones J Pharm 31:171\u2013180","journal-title":"Indones J Pharm"},{"key":"3948_CR55","doi-asserted-by":"crossref","unstructured":"Raj SP, Solomon PR, Thangaraj B, 2022. Malvaceae. Biodiesel from Flowering Plants 1, 385\u2013405","DOI":"10.1007\/978-981-16-4775-8_23"},{"key":"3948_CR56","doi-asserted-by":"publisher","DOI":"10.3389\/fevo.2015.00120","volume":"3","author":"JE Richardson","year":"2015","unstructured":"Richardson JE, Whitlock BA, Meerow AW, Madri\u00f1\u00e1n S (2015) The age of chocolate: a diversification history of Theobroma and Malvaceae. Front Ecol Evol 3:120","journal-title":"Front Ecol Evol"},{"key":"3948_CR57","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1016\/j.cels.2018.01.001","volume":"6","author":"JT Robinson","year":"2018","unstructured":"Robinson JT, Turner D, Durand NC, Thorvaldsd\u00f3ttir H, Mesirov JP, Aiden EL (2018) Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Syst 6:256-258.e1","journal-title":"Cell Syst"},{"key":"3948_CR58","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","volume":"1962","author":"M Seppey","year":"2019","unstructured":"Seppey M, Manni M, Zdobnov EM (2019) BUSCO: assessing genome assembly and annotation completeness. Methods Mol Biol 1962:227\u2013245","journal-title":"Methods Mol Biol"},{"key":"3948_CR59","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1186\/s13059-015-0831-x","volume":"16","author":"N Servant","year":"2015","unstructured":"Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C-J, Vert J-P, Heard E, Dekker J, Barillot E (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16:259","journal-title":"Genome Biol"},{"key":"3948_CR60","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.100832","volume":"5","author":"L Shao","year":"2024","unstructured":"Shao L, Jin S, Chen J, Yang G, Fan R, Zhang Z, Deng Q, Han J, Ma X, Dong Z (2024) High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development. Plant Commun 5:100832","journal-title":"Plant Commun"},{"key":"3948_CR61","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009730","volume":"18","author":"A Shumate","year":"2022","unstructured":"Shumate A, Wong B, Pertea G, Pertea M (2022) Improved transcriptome assembly using a hybrid of long and short reads with StringTie. PLoS Comput Biol 18:e1009730","journal-title":"PLoS Comput Biol"},{"key":"3948_CR62","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1016\/S0140-6736(15)01156-3","volume":"387","author":"M Springmann","year":"2016","unstructured":"Springmann M, Mason-D\u2019Croz D, Robinson S, Garnett T, Godfray HC, Gollin D, Rayner M, Ballon P, Scarborough P (2016) Global and regional health effects of future food production under climate change: a modelling study. Lancet 387:1937\u20131946","journal-title":"Lancet"},{"key":"3948_CR63","doi-asserted-by":"publisher","first-page":"W435","DOI":"10.1093\/nar\/gkl200","volume":"34","author":"M Stanke","year":"2006","unstructured":"Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435\u2013W439","journal-title":"Nucleic Acids Res"},{"key":"3948_CR64","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1007\/978-1-0716-1134-0_4","volume":"2250","author":"W Su","year":"2021","unstructured":"Su W, Ou S, Hufford MB, Peterson T (2021) A tutorial of EDTA: extensive de novo TE annotator. Methods Mol Biol 2250:55\u201367","journal-title":"Methods Mol Biol"},{"key":"3948_CR65","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1016\/j.molp.2022.10.018","volume":"15","author":"P Sun","year":"2022","unstructured":"Sun P, Jiao B, Yang Y, Shan L, Li T, Li X, Xi Z, Wang X, Liu J (2022) WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol Plant 15:1841\u20131851","journal-title":"Mol Plant"},{"key":"3948_CR66","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2313921121","volume":"121","author":"P Sun","year":"2024","unstructured":"Sun P, Lu Z, Wang Z, Wang S, Zhao K, Mei D, Yang J, Yang Y, Renner SS, Liu J (2024) Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family. Proc Natl Acad Sci U S A 121:e2313921121","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3948_CR67","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv227","volume":"43","author":"S Tang","year":"2015","unstructured":"Tang S, Lomsadze A, Borodovsky M (2015) Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 43:e78","journal-title":"Nucleic Acids Res"},{"key":"3948_CR68","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.211","volume":"3","author":"H Tang","year":"2024","unstructured":"Tang H, Krishnakumar V, Zeng X, Xu Z, Taranto A, Lomas JS, Zhang Y, Huang Y, Wang Y, Yim WC et al (2024) JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3:e211","journal-title":"iMeta"},{"key":"3948_CR69","first-page":"23","volume":"45","author":"F Tapia-Pastrana","year":"2007","unstructured":"Tapia-Pastrana F (2007) Citogen\u00e9tica de Guazuma ulmifolia var. ulmifolia (Sterculiaceae). Darwiniana Nueva Ser 45:23\u201327","journal-title":"Darwiniana Nueva Ser"},{"key":"3948_CR70","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-41","volume":"4","author":"RL Tatusov","year":"2003","unstructured":"Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41","journal-title":"BMC Bioinform"},{"key":"3948_CR71","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.1038\/ng.3972","volume":"49","author":"BT Teh","year":"2017","unstructured":"Teh BT, Lim K, Yong CH, Ng CCY, Rao SR, Rajasegaran V, Lim WK, Ong CK, Chan K, Cheng VKY et al (2017) The draft genome of tropical fruit durian (Durio zibethinus). Nat Genet 49:1633\u20131641","journal-title":"Nat Genet"},{"key":"3948_CR72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/boj.12385","volume":"181","author":"The Angiosperm Phylogeny Group","year":"2016","unstructured":"The Angiosperm Phylogeny Group (2016) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc 181:1\u201320","journal-title":"Bot J Linn Soc"},{"key":"3948_CR73","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1093\/aob\/mcx078","volume":"120","author":"CM Vicient","year":"2017","unstructured":"Vicient CM, Casacuberta JM (2017) Impact of transposable elements on polyploid plant genomes. Ann Bot 120:195\u2013207","journal-title":"Ann Bot"},{"key":"3948_CR74","first-page":"135","volume":"39","author":"C Walker","year":"2021","unstructured":"Walker C (2021) A survey of succulents of the mallow family (Malvaceae). CactusWorld 39:135\u2013148","journal-title":"CactusWorld"},{"key":"3948_CR75","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 8:77\u201380","journal-title":"Genom Proteom Bioinform"},{"key":"3948_CR76","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1038\/ng.2371","volume":"44","author":"K Wang","year":"2012","unstructured":"Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S et al (2012) The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44:1098\u20131103","journal-title":"Nat Genet"},{"key":"3948_CR77","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1111\/tpj.16499","volume":"117","author":"J Wang","year":"2024","unstructured":"Wang J, Xie W, Si F, He Z, Wang X, Shao S, Shi S, Guo Z (2024) Evolution of sea-surfing plant propagule as revealed by the genomes of Heritiera mangroves. Plant J 117:432\u2013448","journal-title":"Plant J"},{"key":"3948_CR78","first-page":"420","volume":"26","author":"BA Whitlock","year":"2001","unstructured":"Whitlock BA, Bayer C, Baum DA (2001) Phylogenetic relationships and floral evolution of the Byttnerioideae (\u201cSterculiaceae\u201d or Malvaceae s.l.) based on sequences of the chloroplast gene, ndhF. Syst Bot 26:420\u2013437","journal-title":"Syst Bot"},{"key":"3948_CR79","doi-asserted-by":"publisher","DOI":"10.1016\/j.xplc.2024.101046","volume":"5","author":"D Xu","year":"2024","unstructured":"Xu D, Yang J, Wen H, Feng W, Zhang X, Hui X, Yue J, Xu Y, Chen F, Pan W (2024) CentIER: accurate centromere identification for plant genomes. Plant Commun 5:101046","journal-title":"Plant Commun"},{"key":"3948_CR80","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586\u20131591","journal-title":"Mol Biol Evol"},{"key":"3948_CR81","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1016\/j.jgg.2024.05.006","volume":"52","author":"CA Yang","year":"2025","unstructured":"Yang CA, Hu SY, Ge J, Wang H, Wang Y, Gu C, Xue JY (2025) Frequent polyploidization events in Hibiscus shaped its karyotype and species diversity. J Genet Genomics 52:864\u2013867","journal-title":"J Genet Genomics"},{"key":"3948_CR82","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1038\/s41477-024-01755-3","volume":"10","author":"X Zeng","year":"2024","unstructured":"Zeng X, Yi Z, Zhang X, Du Y, Li Y, Zhou Z, Chen S, Zhao H, Yang S, Wang Y et al (2024) Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. Nat Plants 10:1184\u20131200","journal-title":"Nat Plants"},{"key":"3948_CR83","doi-asserted-by":"publisher","first-page":"2235","DOI":"10.1111\/pbi.13652","volume":"19","author":"L Zhang","year":"2021","unstructured":"Zhang L, Ma X, Zhang X, Xu Y, Ibrahim AK, Yao J, Huang H, Chen S, Liao Z, Zhang Q et al (2021) Reference genomes of the two cultivated jute species. Plant Biotechnol J 19:2235\u20132248","journal-title":"Plant Biotechnol J"}],"container-title":["Plant Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00299-026-03948-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00299-026-03948-w","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00299-026-03948-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T10:03:08Z","timestamp":1789639388000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00299-026-03948-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,28]]},"references-count":83,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["3948"],"URL":"https:\/\/doi.org\/10.1007\/s00299-026-03948-w","relation":{},"ISSN":["0721-7714","1432-203X"],"issn-type":[{"value":"0721-7714","type":"print"},{"value":"1432-203X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,28]]},"assertion":[{"value":"25 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no conflict of interest in this work.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"273"}}