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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The DUF789 protein family comprises conserved domain proteins in plants, most of which remain functionally uncharacterized despite their involvement in growth, development, and stress responses. Moreover, systematic identification of the DUF789 family in tomato (Solanum lycopersicum L.) has not been reported. In this study, 11 SlDUF789 members were identified from the tomato genome, unevenly distributed across seven chromosomes, with members within the same subgroup sharing similar exon\u2013intron structures and conserved motifs. Promoter analysis revealed the enrichment of cis-acting elements associated with light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis revealed diverse expression patterns across tissues: most SlDUF789 members exhibited relatively high expression levels in reproductive tissues, whereas SlDUF789-7 was broadly expressed across all tissues, with elevated expression in fully open flowers and red-ripe fruits. Under stress and hormone treatments, SlDUF789-7 exhibited the highest induction under ABA and salt stress; SlDUF789-8 under MeJA and PEG; and SlDUF789-11 under SA and low-light. Notably, SlDUF789-7 responded strongly across all treatments, whereas SlDUF789-11 showed sustained upregulation under low-light stress. This study provides the first systematic characterization of the SlDUF789 gene family in tomato and establishes a foundation for future research on their biological functions and potential roles in stress responses.<\/jats:p>","DOI":"10.3390\/ijms27188014","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T09:24:02Z","timestamp":1788945842000},"page":"8014","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The SlDUF789 Gene Family in Tomato: Genome-Wide Identification and Responsiveness to Hormonal and Abiotic Stress Signals"],"prefix":"10.3390","volume":"27","author":[{"given":"Wenbing","family":"Zou","sequence":"first","affiliation":[{"name":"College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"given":"Xinfang","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"given":"Zhipeng","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7404-2145","authenticated-orcid":false,"given":"Weibiao","family":"Liao","sequence":"additional","affiliation":[{"name":"College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1107\/S1744309110001685","article-title":"DUFs: Families in search of function","volume":"66","author":"Bateman","year":"2010","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e17537","DOI":"10.7717\/peerj.17537","article-title":"Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato","volume":"12","author":"Li","year":"2024","journal-title":"PeerJ"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.1093\/pcp\/pct070","article-title":"The Arabidopsis DUF231 domain-containing protein ESK1 mediates 2-O- and 3-O-acetylation of xylosyl residues in xylan","volume":"54","author":"Yuan","year":"2013","journal-title":"Plant Cell Physiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"14253","DOI":"10.1073\/pnas.1208097109","article-title":"4-O-Methylation of glucuronic acid in Arabidopsis glucuronoxylan is catalyzed by a domain of unknown function family 579 protein","volume":"109","author":"Urbanowicz","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1111\/j.1365-313X.2003.01993.x","article-title":"Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development","volume":"37","author":"Zhao","year":"2004","journal-title":"Plant J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"483","DOI":"10.4161\/psb.6.4.14784","article-title":"Novel protein-protein interaction family proteins involved in chloroplast movement response","volume":"6","author":"Kodama","year":"2011","journal-title":"Plant Signal. Behav."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.plantsci.2016.10.007","article-title":"The cell wall DUF642 At2g41800 (TEB) protein is involved in hypocotyl cell elongation","volume":"253","year":"2016","journal-title":"Plant Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s40626-019-00146-w","article-title":"Characterization of an Arabidopsis thaliana DUF761-containing protein with a potential role in development and defense responses","volume":"31","author":"Zhang","year":"2019","journal-title":"Theor. Exp. Plant Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.bbrc.2012.02.131","article-title":"Suppression of Arabidopsis RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces tolerance to ABA-mediated drought stress","volume":"420","author":"Kim","year":"2012","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1111\/j.1365-313X.2006.02994.x","article-title":"Arabidopsis ESK1 encodes a novel regulator of freezing tolerance","volume":"49","author":"Xin","year":"2007","journal-title":"Plant J."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1111\/jipb.12376","article-title":"OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice","volume":"58","author":"Guo","year":"2016","journal-title":"J. Integr. Plant Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1007\/s12374-016-0180-7","article-title":"Over-expression of a DUF1644 protein gene, SIDP361, enhances tolerance to salt stress in transgenic rice","volume":"59","author":"Li","year":"2016","journal-title":"J. Plant Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1080\/13102818.2017.1289122","article-title":"Molecular characterization and function analysis of the rice OsDUF946 family","volume":"31","author":"Li","year":"2017","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Zhou, X., Zhu, X., Shao, W., Song, J., Jiang, W., He, Y., Yin, J., Ma, D., and Qiao, Y. (2020). Genome-wide mining of wheat DUF966 gene family provides new insights into salt stress responses. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.569838"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1007\/s11105-012-0549-9","article-title":"A novel ABA-responsive TaSRHP gene from wheat contributes to enhanced resistance to salt stress in Arabidopsis thaliana","volume":"31","author":"Hou","year":"2013","journal-title":"Plant Mol. Biol. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1016\/S2095-3119(17)61897-5","article-title":"Overexpression of AmDUF1517 enhanced tolerance to salinity, drought, and cold stress in transgenic cotton","volume":"17","author":"Hao","year":"2018","journal-title":"J. Integr. Agric."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Liu, E., Li, Z., Luo, Z., Xu, L., Jin, P., Ji, S., Zhou, G., Wang, Z., Zhou, Z., and Zhang, H. (2023). Genome-wide identification of DUF668 gene family and expression analysis under drought and salt stresses in sweet potato [Ipomoea batatas (L.) Lam]. Genes, 14.","DOI":"10.3390\/genes14010217"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Han, S., Han, X., Qi, C., Guo, F., Yin, J., Liu, Y., and Zhu, Y. (2024). Genome-wide identification of DUF668 gene family and expression analysis under F. solani, chilling, and waterlogging stresses in Zingiber officinale. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25020929"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"The Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635\u2013641.","DOI":"10.1038\/nature11119"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Aoki, K., Yano, K., Suzuki, A., Kawamura, S., Sakurai, N., Suda, K., Kurabayashi, A., Suzuki, T., Tsugane, T., and Watanabe, M. (2010). Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genom., 11.","DOI":"10.1186\/1471-2164-11-210"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1146\/annurev.arplant.59.032607.092911","article-title":"Mechanisms of salinity tolerance","volume":"59","author":"Munns","year":"2008","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1146\/annurev.arplant.53.091401.143329","article-title":"Salt and drought stress signal transduction in plants","volume":"53","author":"Zhu","year":"2002","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4388","DOI":"10.1093\/plcell\/koac254","article-title":"A SlCLV3-SlWUS module regulates auxin and ethylene homeostasis in low light-induced tomato flower abscission","volume":"34","author":"Cheng","year":"2022","journal-title":"Plant Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"103478","DOI":"10.1016\/j.jksus.2024.103478","article-title":"Genome-wide and expression analysis to understand the DUF789 gene family during development of Arabidopsis thaliana","volume":"36","author":"Zaynab","year":"2024","journal-title":"J. King Saud Univ. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Hamid, R., Panahi, B., Ghorbanzadeh, Z., Jacob, F., Zeinalabedini, M., and Ghaffari, M.R. (2025). Genome-wide identification and characterization of DUF789 genes in cotton: Implications for fibre development. BMC Plant Biol., 25.","DOI":"10.1186\/s12870-025-07258-3"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.sajb.2025.02.033","article-title":"Genome-wide analysis and expression pattern profiling of the DUF789 gene family in soybean (Glycine max L.)","volume":"180","author":"Zaynab","year":"2025","journal-title":"S. Afr. J. Bot."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1104\/pp.108.122457","article-title":"Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli","volume":"148","author":"Hanada","year":"2008","journal-title":"Plant Physiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e70370","DOI":"10.1111\/tpj.70370","article-title":"Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants","volume":"123","author":"Yang","year":"2025","journal-title":"Plant J."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Fischer, I., Dainat, J., Ranwez, V., Gl\u00e9min, S., Dufayard, J.F., and Chantret, N. (2014). Impact of recurrent gene duplication on adaptation of plant genomes. BMC Plant Biol., 14.","DOI":"10.1186\/1471-2229-14-151"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"108493","DOI":"10.1016\/j.plaphy.2024.108493","article-title":"Characterization of the DUF868 gene family in Nicotiana and functional analysis of NtDUF868-E5 involved in pigment metabolism","volume":"208","author":"Cao","year":"2024","journal-title":"Plant Physiol. Biochem."},{"key":"ref_32","first-page":"691","article-title":"Advances in identification and synthesis of promoter elements in higher plants","volume":"59","author":"Song","year":"2024","journal-title":"Chin. Bull. Bot."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2136","DOI":"10.1093\/pcp\/pcr143","article-title":"An ABRE promoter sequence is involved in osmotic stress-responsive expression of the DREB2A gene, which encodes a transcription factor regulating drought-inducible genes in Arabidopsis","volume":"52","author":"Kim","year":"2011","journal-title":"Plant Cell Physiol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Gangappa, S.N., Maurya, J.P., Yadav, V., and Chattopadhyay, S. (2013). The regulation of the Z- and G-box containing promoters by light signaling components, SPA1 and MYC2, in Arabidopsis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0062194"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Zhong, H., Zhang, H., Guo, R., Wang, Q., Huang, X., Liao, J., Li, Y., Huang, Y., and Wang, Z. (2019). Characterization and functional divergence of a novel DUF668 gene family in rice based on comprehensive expression patterns. Genes, 10.","DOI":"10.3390\/genes10120980"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Zhao, J., Wang, P., Gao, W., Long, Y., Wang, Y., Geng, S., Su, X., Jiao, Y., Chen, Q., and Qu, Y. (2021). Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07716-w"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"15682","DOI":"10.1073\/pnas.2535513100","article-title":"The early stages of duplicate gene evolution","volume":"100","author":"Moore","year":"2003","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: Interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Zhang, R., Liang, K., Qiu, Z., Shi, D., He, S., Zhu, G., Xu, B., Hussain, I., Huang, J., and Gulzar, R.M.A. (2026). CBL Gene Family in Brassica napus: Genome-Wide and Expression Profiling in Response to Phytohormones Under Diverse Stress Conditions. Agriculture, 16.","DOI":"10.3390\/agriculture16101088"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: A \u201cOne for All, All for One\u201d Bioinformatics Platform for Biological Big-Data Mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_41","first-page":"681","article-title":"SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments","volume":"11","author":"Geourjon","year":"1995","journal-title":"Comput. Appl. Biosci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: Homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/nar\/30.1.325","article-title":"PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences","volume":"30","author":"Lescot","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_45","first-page":"418","article-title":"Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions","volume":"3","author":"Nei","year":"1986","journal-title":"Mol. Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Gulzar, R.M.A., Ahmad, N., Zhao, X., Zhao, T., Zhan, J., Yu, H., Javaid, M.H., Munir, R., Nazir, M.M., and Hussain, I. (2026). Genome-Wide Identification and Expression Profiling of PYL Genes in Brassica napus Under ABA and Drought-Stress Treatments. Stresses, 6.","DOI":"10.3390\/stresses6030041"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Zhu, Y., Kong, Y., Liu, X., Cui, A., Chang, C., Hou, X., and Liao, W. (2026). The FPF Gene Family in Tomato: Genome-Wide Identification and the Role of SlFPF1 in Gibberellin-Dependent Growth. Agriculture, 16.","DOI":"10.3390\/agriculture16020258"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Ma, Y., Li, Y., Wang, F., Qing, Q., Deng, C., Wang, H., and Song, Y. (2025). Screening and Identification of Drought-Tolerant Genes in Tomato (Solanum lycopersicum L.) Based on RNA-Seq Analysis. Plants, 14.","DOI":"10.3390\/plants14101471"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"110840","DOI":"10.1016\/j.plaphy.2025.110840","article-title":"Genome-wide analysis of the SlEIN3\/EIL gene family and the roles of SlEIL3 in enhancing salt tolerance in tomatoes","volume":"230","author":"Liu","year":"2026","journal-title":"Plant Physiol. Biochem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394C(T) method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2307\/3001478","article-title":"Multiple range and multiple F tests","volume":"11","author":"Duncan","year":"1955","journal-title":"Biometrics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8014\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T04:25:43Z","timestamp":1789100743000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/18\/8014"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":51,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27188014"],"URL":"https:\/\/doi.org\/10.3390\/ijms27188014","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,9]]}}}