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Bioinformatic analyses were used to predict rice (Oryza sativa L.) miRNAs that regulate gene expression during interactions with the pathogenic fungi Rhizoctonia solani and Magnaporthe oryzae, and the symbiotic fungus Rhizophagus irregularis. Up-regulated rice miRNAs were linked to fungal targets enriched in KEGG/GO pathways affecting metabolism, signaling, transport, and essential cellular processes.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/rice-mirna-mediated-trans-kingdom-gene-regulation-in-pathogenic-and-symbiotic-fungal-interactions/457643/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/rice-mirna-mediated-trans-kingdom-gene-regulation-in-pathogenic-and-symbiotic-fungal-interactions/457643.png","ImageObject",300,407,{"name":92,"@type":93},"pop out","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-08","2026-09-30",true,{"@type":102,"interactionType":103,"userInteractionCount":44},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"What was the main goal of the study on rice miRNAs?","Question",{"text":112,"@type":113},"To predict how rice miRNAs regulate gene expression during interactions with both pathogenic fungi and a symbiotic fungus, using bioinformatic analyses.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"Which fungal and symbiotic organisms were investigated?",{"text":117,"@type":113},"The pathogens Rhizoctonia solani and Magnaporthe oryzae, and the symbiont Rhizophagus irregularis.",{"name":119,"@type":110,"acceptedAnswer":120},"What do KEGG and GO enrichment results suggest about miRNA targets?",{"text":121,"@type":113},"They suggest rice miRNAs can target fungal genes involved in pathogen metabolism, genetic information processing, signaling, transport, catabolism, and other essential cellular processes, potentially affecting virulence and survival.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},457643,1790814718,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":133,"doc_module":4,"category_id":39,"category_name":40,"doc_title":65,"doc_description":67,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":44,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":139,"language":140,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":141,"faqs":142,"seo_title":143,"seo_description":67,"update_tm":144,"read_time":145},962090760408,"https://ap-avatar.wpscdn.com/davatar_085a072bc5b1113ac321206ff7593b45","Jannesar etal. BMC Genomics (2026) 27:17 BMC Genomics  \n[https://doi.org/10.1186/s12864-025-12386-z](https://doi.org/10.1186/s12864-025-12386-z)  \nRESEARCH Open Access  \nRice miRNA-mediated trans-kingdom gene  regulation in pathogenic and symbiotic fungal interactions  \nMasoomeh Jannesar 1*, Bahram Bassami2, Ghazal Dalir2, Soheil Sheikhzadeh2, Javad Tabrizchi3 and Seyed Mahdi Seyedi 1,3*  \nAbstract  \nBackground The trans-kingdom movement of microRNAs (miRNAs) is a key regulatory mechanism in plant biotic interactions, influencing and modulating both pathogenic virulence and symbiotic relationships. This study employed bioinformatic analysis to predict the role of rice (Oryza sativa L.) miRNAs in regulating gene expression during interactions with the pathogenic fungi Rhizoctonia solani (R. solani) and Magnaporthe oryzae (M. oryzae), as well as the symbiotic fungus Rhizophagus irregularis (R. irregularis) .  \nResults Previously reported and up-regulated rice miRNAs were identified from the literature during inoculation, and their target genes were predicted in the fungal transcriptomes. The KEGG pathway and GO enrichment analyses revealed that rice miRNAs could target genes crucial for pathogen metabolism (e. g., carbohydrate, amino acid, lipid, and xenobiotic), genetic information processing, and essential cellular processes (e. g., signal transduction, transport, catabolism, and cell growth and death), potentially impairing fungal virulence and survival. The osa-miR171 family is predicted to regulate R. irregularis genes involved in protein serine/threonine kinase activity, antiporter activity, cell division, TAP complex binding, and O-acetyl homoserine sulfhydrylase activity during symbiosis. Additionally, the osa-miR171 family targets key rice genes such as phosphate transporter, NSP2, and SCR, involved in nutrient transport, common symbiosis signaling, and root development, respectively, which are likely important for forming and regulating a symbiotic relationship. The qRT‒PCR results confirmed the up-regulation of osa-miR171h (symbiosisrelated) and osa-miR167d-5p (pathogen-responsive) in rice roots inoculated with R. irregularis.  \nConclusions These findings highlight the significant role of trans-kingdom RNA regulation in plant–microbe interactions, contributing to understanding the molecular regulation, distinctions, and similarities between pathogenic and symbiotic relationships in plants. This initial study performs the first comparative trans-kingdomsRNA analysis in rice, successfully predicting and distinguishing the molecular mechanisms that drive virulence versus mutualism. This work also lays the groundwork for developing novel strategies to enhance plant disease resistance, foster beneficial symbiotic interactions, and ultimately boost agricultural yields.  \n*Correspondence: Masoomeh Jannesar [jannesar@ut.ac.ir](jannesar@ut.ac.ir)[ ](jannesar@ut.ac.ir)Seyed Mahdi Seyedi [Seyedi@nigeb.ac.ir](Seyedi@nigeb.ac.ir)  \nFull list of author information is available at the end of the article  \n© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyrig","cbCaiptHt6pZRQTX","https://ap.wps.com/l/cbCaiptHt6pZRQTX","pdf",2245437,13,"English","# Abstract\n## Background\n## Results\n## Conclusions\n# Background\n## Rice as a food source and biotic stress threats\n## Major rice fungal diseases and model interactions","[{\"question\":\"What was the main goal of the study on rice miRNAs?\",\"answer\":\"To predict how rice miRNAs regulate gene expression during interactions with both pathogenic fungi and a symbiotic fungus, using bioinformatic analyses.\"},{\"question\":\"Which fungal and symbiotic organisms were investigated?\",\"answer\":\"The pathogens Rhizoctonia solani and Magnaporthe oryzae, and the symbiont Rhizophagus irregularis.\"},{\"question\":\"What do KEGG and GO enrichment results suggest about miRNA targets?\",\"answer\":\"They suggest rice miRNAs can target fungal genes involved in pathogen metabolism, genetic information processing, signaling, transport, catabolism, and other essential cellular processes, potentially affecting virulence and survival.\"}]","Rice miRNA-mediated trans-kingdom gene regulation in pathogenic and symbiotic fungal interactions | PDF",1790750048,33]