{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,14]],"date-time":"2026-11-14T09:47:13Z","timestamp":1794649633298,"version":"4.9.1"},"reference-count":62,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T00:00:00Z","timestamp":1779753600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Project of Fund for Stable Support to Agricultural Sci-Tech Renovation","award":["xjnkywdzc-2025001-98"],"award-info":[{"award-number":["xjnkywdzc-2025001-98"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Alternaria alternata causes major postharvest losses in melons. This dual RNA-seq study analyzed transcriptomic dynamics in both A. alternata strain A2022 and melon during infection. Genomic analysis revealed two conditionally dispensable chromosomes (CDCs) containing host-specific toxin genes, including a T1PKS cluster for \u03b2enone biosynthesis. Fungal transcriptomics identified upregulated virulence pathways: MAPK signaling (18 genes), autophagy (17 genes), and lipid metabolism. Melon mounted a biphasic defense: early lignin deposition via phenylpropanoid biosynthesis (15 genes) and late jasmonic acid\/MAPK-mediated responses. Competitive nutrient acquisition emerged, with fungal amino acid transporters opposing host nitrogen metabolism. These findings reveal A. alternata\u2019s genomic plasticity and melon\u2019s layered resistance, suggesting RNAi-based silencing of CDC virulence genes or breeding for enhanced lignin\/jasmonate pathways as sustainable control strategies.<\/jats:p>","DOI":"10.3390\/foods15111876","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T11:02:51Z","timestamp":1779793371000},"page":"1876","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Dual RNA-Seq Reveals Molecular Interactions Between Alternaria alternata and Cucumis melo During Postharvest Infection"],"prefix":"10.3390","volume":"15","author":[{"given":"Yujia","family":"Bai","sequence":"first","affiliation":[{"name":"Institute of Food Science and Technology, Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, Urumqi 830091, China"},{"name":"Xinjiang Key Laboratory of Processing and Preservation of Agricultural Products, Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangfeng","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Wu","sequence":"additional","affiliation":[{"name":"Institute of Food Science and Technology, Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, Urumqi 830091, China"},{"name":"Xinjiang Key Laboratory of Processing and Preservation of Agricultural Products, Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, Urumqi 830091, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyue","family":"Kong","sequence":"additional","affiliation":[{"name":"College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liuchun","family":"Du","sequence":"additional","affiliation":[{"name":"College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3920\/WMJ2009.1145","article-title":"Alternaria toxins and plant diseases: An overview of origin, occurrence and risks","volume":"2","author":"Logrieco","year":"2009","journal-title":"World Mycotoxin J."},{"key":"ref_2","unstructured":"Food and Agriculture Organization of the United Nations (FAO) (2025, December 31). FAOSTAT: Production Crops. Available online: http:\/\/www.fao.org\/faostat\/en\/#data\/QC."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"347","DOI":"10.2307\/3761094","article-title":"The Genus Alternaria: Biology, epidemiology, and pathogenicity","volume":"89","author":"Rotem","year":"1997","journal-title":"Mycologia"},{"key":"ref_4","first-page":"558","article-title":"Alternaria section Alternaria: Species, formae speciales and pathotypes of worldwide importance","volume":"107","author":"Woudenberg","year":"2015","journal-title":"Mycologia"},{"key":"ref_5","first-page":"1450","article-title":"Identification of novel virulence factors associated with signal transduction pathways in Alternaria brassicicola","volume":"20","author":"Cho","year":"2007","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Meena, M., Gupta, S.K., Swapnil, P., Zehra, A., Dubey, M.K., and Upadhyay, R.S. (2017). Alternaria toxins: Potential virulence factors and genes related to pathogenesis. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.01451"},{"key":"ref_7","first-page":"42","article-title":"An update on the occurrence and health risk of mycotoxins in foods","volume":"14","author":"Escriva","year":"2017","journal-title":"Curr. Opin. Food Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/j.1574-6976.2012.00350.x","article-title":"Host-selective toxins produced by the plant pathogenic fungus Alternaria alternata","volume":"37","author":"Tsuge","year":"2013","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Hu, J., Chen, C., Peever, T., Dang, H., Lawrence, C., and Mitchell, T. (2012). Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-171"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1111\/mpp.12927","article-title":"Related mobile pathogenicity chromosomes in Fusarium oxysporum determine host range on cucurbits","volume":"21","author":"Li","year":"2020","journal-title":"Mol. Plant Pathol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.fgb.2015.08.010","article-title":"Mind the gap; seven reasons to close fragmented genome assemblies","volume":"90","author":"Thomma","year":"2016","journal-title":"Fungal Genet. Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"11446","DOI":"10.1073\/pnas.1714821114","article-title":"Diel cycling and long-term persistence of viruses in the ocean\u2019s euphotic zone","volume":"114","author":"Aylward","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Dang, H.X., Pryor, B., Peever, T., and Lawrence, C.B. (2015). The Alternaria genomes database: A comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC Genom., 16.","DOI":"10.1186\/s12864-015-1430-7"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41576-021-00326-y","article-title":"Cross-species RNA-seq for deciphering host\u2013microbe interactions","volume":"22","author":"Westermann","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"127","DOI":"10.21775\/cimb.027.127","article-title":"Dual RNA-seq to Elucidate the Plant\u2013Pathogen Duel","volume":"27","author":"Naidoo","year":"2018","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1104\/pp.106.079467","article-title":"Reactive oxygen species signaling in response to pathogens","volume":"141","author":"Torres","year":"2006","journal-title":"Plant Physiol."},{"key":"ref_17","first-page":"17413","article-title":"Transcriptome analysis of apple (Malus \u00d7 domestica) in response to Botryosphaeria dothidea infection","volume":"7","author":"Kumar","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Wang, N., Pierson, E.A., Setubal, J.C., Xu, J., Levy, J.G., Zhang, Y., Li, J., Rangel, L.T., and Martins, J. (2016). Transcriptome profiling of Huanglongbing (HLB) tolerant and susceptible citrus plants reveals the role of basal resistance in HLB tolerance. Front. Plant Sci., 7.","DOI":"10.3389\/fpls.2016.00933"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1094\/MPMI-02-15-0039-R","article-title":"Analysis of the molecular dialogue between gray mold (Botrytis cinerea) and grapevine (Vitis vinifera) reveals a clear shift in defense mechanisms during berry ripening","volume":"28","author":"Kelloniemi","year":"2015","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1094\/MPMI-08-10-0187","article-title":"Functional analysis of the Asian soybean rust resistance pathway mediated by Rpp2","volume":"24","author":"Pandey","year":"2011","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/nature16547","article-title":"Dual RNA-seq unveils noncoding RNA functions in host\u2013pathogen interactions","volume":"529","author":"Westermann","year":"2016","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., and Young, S.K. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Waterhouse","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Brent, M.R. (2005). Gene finding in novel genomes. BMC Bioinform., 6.","DOI":"10.1186\/1471-2105-6-131"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e89","DOI":"10.1093\/nar\/gkw092","article-title":"Using intron position conservation for homology-based gene prediction","volume":"44","author":"Keilwagen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using evidencemodeler and the program to assemble spliced alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., and Nikolskaya, A.N. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinform., 4.","DOI":"10.1186\/1471-2105-4-41"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Eddy, S.R. (2011). Accelerated profile HMM searches. PLoS Comput. Biol., 7.","DOI":"10.1371\/journal.pcbi.1002195"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"D372","DOI":"10.1093\/nar\/gkv1103","article-title":"The Transporter Classification Database (TCDB): Recent advances","volume":"44","author":"Saier","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_37","first-page":"D613","article-title":"PHI-base: The pathogen\u2013host interactions database","volume":"48","author":"Urban","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1093\/bioinformatics\/btm268","article-title":"The Cytochrome P450 Engineering Database: A navigation and prediction tool for the cytochrome P450 protein family","volume":"23","author":"Fischer","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_39","first-page":"bas032","article-title":"DFVF: Database of fungal virulence factors","volume":"2012","author":"Lu","year":"2012","journal-title":"Database J. Biol. Databases Curation"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gkn663","article-title":"Carbohydrate-active enzymes: An integrated database approach","volume":"37","author":"Cantarel","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1094\/MPMI-21-10-1325","article-title":"The yeast signal sequence trap identifies secreted proteins of the hemibiotrophic corn pathogen Colletotrichum graminicola","volume":"21","author":"Krijger","year":"2008","journal-title":"Mol. Plant Microbe Interact."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014A Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1093\/bioinformatics\/btp612","article-title":"DEGseq: An R package for identifying differentially expressed genes from RNA-seq data","volume":"26","author":"Wang","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/btl140","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume":"22","author":"Alexa","year":"2006","journal-title":"Bioinformatics"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1093\/nar\/gkr483","article-title":"KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases","volume":"39","author":"Xie","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1128\/EC.00153-06","article-title":"BcSAK1, a stress-activated mitogen-activated protein kinase, is involved in vegetative differentiation and pathogenicity in Botrytis cinerea","volume":"6","author":"Ellendorf","year":"2007","journal-title":"Eukaryot. Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1492","DOI":"10.1094\/MPMI-22-12-1492","article-title":"Triacylglyceride metabolism by Fusarium graminearum during colonization and sexual development on wheat","volume":"22","author":"Guenther","year":"2009","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_48","first-page":"1303","article-title":"Jasmonates: Biosynthesis, metabolism, and signaling by proteins activating and repressing transcription","volume":"68","author":"Wasternack","year":"2017","journal-title":"J. Exp. Bot."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1146\/annurev-phyto-082712-102314","article-title":"MAPK cascades in plant disease resistance signaling","volume":"51","author":"Meng","year":"2013","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_50","first-page":"1573","article-title":"Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens","volume":"10","author":"Thomma","year":"1998","journal-title":"Plant Cell"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1146\/annurev.phyto.43.040204.135923","article-title":"Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens","volume":"43","author":"Glazebrook","year":"2005","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_52","first-page":"703","article-title":"Moving nitrogen to the centre of plant defence against pathogens","volume":"119","author":"Mur","year":"2017","journal-title":"Ann. Bot."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1093\/jxb\/eru323","article-title":"Nitrogen metabolism meets phytopathology","volume":"65","author":"Fagard","year":"2014","journal-title":"J. Exp. Bot."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1111\/j.1574-6968.2006.00504.x","article-title":"Nutrition acquisition strategies during fungal infection of plants","volume":"266","author":"Divon","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1146\/annurev-micro-020518-120022","article-title":"Defense and counterdefense during plant-pathogenic oomycete infection","volume":"73","author":"Wang","year":"2019","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_56","first-page":"171","article-title":"The effect of nitrogen on disease development and gene expression in fungal plant pathogens","volume":"29","author":"Snoeijers","year":"2000","journal-title":"Fungal Genet. Biol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/nrmicro2032","article-title":"Under pressure: Investigating the biology of plant infection by Magnaporthe oryzae","volume":"7","author":"Wilson","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1126\/science.291.5501.118","article-title":"Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8","volume":"291","author":"Xiao","year":"2001","journal-title":"Science"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1126\/science.1190859","article-title":"Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants","volume":"329","author":"Kombrink","year":"2010","journal-title":"Science"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1128\/EC.05109-11","article-title":"RNA interference in fungi: Pathways, functions, and applications","volume":"10","author":"Dang","year":"2018","journal-title":"Eukaryot. Cell"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1094\/MPMI-20-5-0492","article-title":"OsWRKY13 mediates rice disease resistance by regulating defense-related genes in salicylate- and jasmonate-dependent signaling","volume":"20","author":"Qiu","year":"2007","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/j.tplants.2012.04.001","article-title":"The rhizosphere microbiome and plant health","volume":"17","author":"Berendsen","year":"2012","journal-title":"Trends Plant Sci."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/11\/1876\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T11:39:27Z","timestamp":1779795567000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/11\/1876"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,26]]},"references-count":62,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2026,6]]}},"alternative-id":["foods15111876"],"URL":"https:\/\/doi.org\/10.3390\/foods15111876","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,26]]}}}