{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:33:52Z","timestamp":1787045632556,"version":"build-2736575974"},"reference-count":46,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32301812"],"award-info":[{"award-number":["32301812"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32301812"],"award-info":[{"award-number":["32301812"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2024M763607"],"award-info":[{"award-number":["2024M763607"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2024M763607"],"award-info":[{"award-number":["2024M763607"]}],"id":[{"id":"https:\/\/ror.org\/0426zh255","id-type":"ROR","asserted-by":"publisher"}]},{"name":"the Postdoctoral Fellowship Program of China Postdoctoral Science Foundation","award":["GZC20233061"],"award-info":[{"award-number":["GZC20233061"]}]},{"award":["GZC20233061"],"award-info":[{"award-number":["GZC20233061"]}],"id":[{"id":"https:\/\/ror.org\/0426zh255","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Key Scientific Research Project of Higher Education of Henan Province","award":["26A180019"],"award-info":[{"award-number":["26A180019"]}]},{"name":"Science and Technology Research Project of Henan Province","award":["262102111152"],"award-info":[{"award-number":["262102111152"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>\u03b2-D-Xylosidases (BXLs) are members of glycoside hydrolase family 3. They play essential roles in cell wall remodeling, plant development, and abiotic stress responses. BXL gene families have been systematically characterized in several crop species. However, a comprehensive analysis of BXL genes in cotton (Gossypium hirsutum), a globally important fiber and oilseed crop, is still lacking. In this study, we performed a genome-wide identification of BXL genes in allotetraploid cotton. A total of 25 GhBXL genes were identified and classified into six phylogenetic clades. Gene structure and conserved domain analyses showed that all GhBXL proteins possess the characteristic tripartite GH3 domain architecture. Chromosomal distribution and synteny analyses indicated that the expansion of the cotton BXL family may be associated with whole-genome duplication and allopolyploidization. Promoter cis-element analysis detected stress-responsive regulatory motifs in the GhBXL promoters, including STRE, W-box, DRE core, and as-1 elements. Under PEG-simulated drought and salt stress, expression profiling, independently confirmed by qRT-PCR, showed distinct temporal response patterns among GhBXL members. Weighted gene co-expression network analysis (WGCNA) further identified GhBXL-8, GhBXL-9, and GhBXL-20 as hub genes in stress-responsive modules. Their co-expressed partners were enriched in transcription factors, kinases, and stress-related proteins. These findings provide a systematic foundation for understanding the evolutionary dynamics and functional roles of BXL genes in cotton. They also highlight candidate genes for future functional investigation.<\/jats:p>","DOI":"10.3390\/biology15161419","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:06:41Z","timestamp":1787044001000},"page":"1419","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification, Evolutionary Analysis, and Expression Profiling of the \u03b2-D-Xylosidase Gene Family in Cotton (Gossypium hirsutum) Under PEG-Simulated Osmotic and Salt Stress"],"prefix":"10.3390","volume":"15","author":[{"given":"Zhenzhen","family":"Wei","sequence":"first","affiliation":[{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anxing","family":"Zhu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Plant-Soil Interactions of MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3712-1322","authenticated-orcid":false,"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangjie","family":"Xiong","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8207-776X","authenticated-orcid":false,"given":"Zhi","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455099, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihan","family":"Xue","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Luoyang Normal University, Luoyang 471934, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455099, China"},{"name":"College of Life Sciences, Luoyang Normal University, Luoyang 471934, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1046\/j.1365-3040.2004.01146.x","article-title":"Identification of genes that are up-regulated in concert during sugar depletion in Arabidopsis","volume":"27","author":"Lee","year":"2004","journal-title":"Plant Cell Environ."},{"key":"ref_2","first-page":"877","article-title":"A \u03b2-D-xylosidase-like gene is expressed during fruit ripening in Japanese pear (Pyrus pyrifolia Nakai)","volume":"50","author":"Itai","year":"1999","journal-title":"J. Exp. Bot."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1007\/s00299-016-1956-4","article-title":"Cell wall-related genes studies on peach cultivars with differential susceptibility to woolliness: Looking for candidates as indicators of chilling tolerance","volume":"35","author":"Genero","year":"2016","journal-title":"Plant Cell Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/pcp\/pcm009","article-title":"Glycosyl hydrolases of cell wall are induced by sugar starvation in Arabidopsis","volume":"48","author":"Lee","year":"2007","journal-title":"Plant Cell Physiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.plantsci.2009.03.015","article-title":"Cloning of the promoter region of \u03b2-xylosidase (FaXyl1) gene and effect of plant growth regulators on the expression of FaXyl1 in strawberry fruit","volume":"177","author":"Bustamante","year":"2009","journal-title":"Plant Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1007\/s13205-020-2061-5","article-title":"Genome-wide identification of BXL genes in Populus trichocarpa and their expression under different nitrogen treatments","volume":"10","author":"Chen","year":"2020","journal-title":"3 Biotech"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bauer, K., Nayem, S., Lehmann, M., Wenig, M., Shu, L.-J., Ranf, S., Geigenberger, P., and Vlot, A.C. (2023). \u03b2-D-XYLOSIDASE 4 modulates systemic immune signaling in Arabidopsis thaliana. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1096800"},{"key":"ref_8","first-page":"87","article-title":"Genome-wide Identification and Expression Analysis of the Rice BXL Gene Family","volume":"41","author":"Hao","year":"2025","journal-title":"Biotechnol. Bull."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Wen, Y., Lai, B., Hu, W., You, M., Wang, L., and Su, T. (2025). Genome-Wide Identification of the BXL Gene Family in Soybean and Expression Analysis Under Salt Stress. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26199534"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Zheng, S., Zhang, X., Lin, C., Guan, P., Liu, L., Su, M., Chen, Q., Yu, R., Jiang, L., and Yao, K. (2025). Genome-Wide Identification of beta-D-Xylosidase Gene Family in Potato and Functional Analysis Under Alkaline Stress. Plants, 14.","DOI":"10.3390\/plants14243790"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/s43017-023-00476-z","article-title":"Environmental impacts of cotton and opportunities for improvement","volume":"4","author":"Zhang","year":"2023","journal-title":"Nat. Rev. Earth Environ."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s42397-023-00154-x","article-title":"High day and night temperatures impact on cotton yield and quality\u2014Current status and future research direction","volume":"6","author":"Saini","year":"2023","journal-title":"J. Cotton Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1002\/moda.16","article-title":"Utilising cottonseed in animal feeding: A dialectical perspective","volume":"1","author":"Wang","year":"2023","journal-title":"Mod. Agric."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e243511","DOI":"10.1590\/1519-6984.243511","article-title":"Physicochemical features, functional characteristics, and health benefits of cottonseed oil: A review","volume":"82","author":"Zia","year":"2022","journal-title":"Braz. J. Biol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Wang, W., Cui, H., Xiao, X., Wu, B., Sun, J., Zhang, Y., Yang, Q., Zhao, Y., Liu, G., and Qin, T. (2022). Genome-Wide Identification of Cotton (Gossypium spp.) Trehalose-6-Phosphate Phosphatase (TPP) Gene Family Members and the Role of GhTPP22 in the Response to Drought Stress. Plants, 11.","DOI":"10.3390\/plants11081079"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Sun, F., Chen, Q., Chen, Q., Jiang, M., Gao, W., and Qu, Y. (2021). Screening of Key Drought Tolerance Indices for Cotton at the Flowering and Boll Setting Stage Using the Dimension Reduction Method. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.619926"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.2135\/cropsci2018.02.0096","article-title":"The Effect of Water Deficit and Waterlogging on the Yield Components of Cotton","volume":"58","author":"Wu","year":"2018","journal-title":"Crop Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.2135\/cropsci2015.08.0477","article-title":"Drought Effects on Cotton Yield and Fiber Quality on Different Fruiting Branches","volume":"56","author":"Wang","year":"2016","journal-title":"Crop Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1111\/jac.12389","article-title":"Drought effects on cotton (Gossypium hirsutum L.) fibre quality and fibre sucrose metabolism during the flowering and boll-formation period","volume":"206","author":"Gao","year":"2020","journal-title":"J. Agron. Crop Sci."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Meshram, J.H., Singh, S.B., Raghavendra, K.P., and Waghmare, V.N. (2022). Drought stress tolerance in cotton: Progress and perspectives. Climate Change and Crop Stress, Academic Press.","DOI":"10.1016\/B978-0-12-816091-6.00005-5"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Chaudhary, M.T., Majeed, S., Rana, I.A., Ali, Z., Jia, Y., Du, X., Hinze, L., and Azhar, M.T. (2024). Impact of salinity stress on cotton and opportunities for improvement through conventional and biotechnological approaches. BMC Plant Biol., 24.","DOI":"10.1186\/s12870-023-04558-4"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Zhang, D., Zhang, Y., Sun, L., Dai, J., and Dong, H. (2023). Mitigating Salinity Stress and Improving Cotton Productivity with Agronomic Practices. Agronomy, 13.","DOI":"10.3390\/agronomy13102486"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"5881","DOI":"10.1007\/s00344-023-10974-5","article-title":"Salicylic Acid Application Improves Photosynthetic Performance and Biochemical Responses to Mitigate Saline Stress in Cotton","volume":"42","author":"Keya","year":"2023","journal-title":"J. Plant Growth Regul."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"D444","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: The protein sequence classification resource in 2025","volume":"53","author":"Blum","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_25","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_26","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3784","DOI":"10.1093\/nar\/gkg563","article-title":"ExPASy: The proteomics server for in-depth protein knowledge and analysis","volume":"31","author":"Gasteiger","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Criscuolo, A., and Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol., 10.","DOI":"10.1186\/1471-2148-10-210"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"Price","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"W587","DOI":"10.1093\/nar\/gkad359","article-title":"Tree Visualization By One Table (tvBOT): A web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_32","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_33","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":"Chen","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: An information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res."},{"key":"ref_36","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":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: A fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: An R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinform."},{"key":"ref_41","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":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"ref_42","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\u0394CT Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1007\/s10722-021-01148-x","article-title":"Molecular breeding and the impacts of some important genes families on agronomic traits, a review","volume":"68","author":"Shahrajabian","year":"2021","journal-title":"Genet. Resour. Crop Evol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"122029","DOI":"10.1016\/j.indcrop.2025.122029","article-title":"GhPMP3-2 positively regulates response to salt stress in upland cotton (Gossypium hirsutum L.)","volume":"236","author":"Wei","year":"2025","journal-title":"Ind. Crops Prod."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Zheng, L., Dai, H., Mu, Y., Li, J., Cheng, Y., and Han, J. (2025). Genome-wide identification and expression analysis of C3H gene family in melon. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1500429"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s13059-019-1650-2","article-title":"Gene duplication and evolution in recurring polyploidization\u2013diploidization cycles in plants","volume":"20","author":"Qiao","year":"2019","journal-title":"Genome Biol."}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/16\/1419\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:22:26Z","timestamp":1787044946000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/15\/16\/1419"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,18]]},"references-count":46,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["biology15161419"],"URL":"https:\/\/doi.org\/10.3390\/biology15161419","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,18]]}}}