Functional & Integrative Genomics最新文献

{"title":"The miRNomics of antiretroviral therapy-induced obesity","authors":"Niska Majumdar,&nbsp;Bishwa R. Pokharel,&nbsp;Abigail Dickerson,&nbsp;Andreea Cruceanu,&nbsp;Smit Rajput,&nbsp;Lok R. Pokhrel,&nbsp;Paul P. Cook,&nbsp;Shaw M. Akula","doi":"10.1007/s10142-025-01585-2","DOIUrl":"10.1007/s10142-025-01585-2","url":null,"abstract":"<div><p>Human immunodeficiency virus (HIV) is a retrovirus that incorporates its genetic material into the host’s chromosome. The resulting diseases and related conditions constitute a global health problem as there are no treatments to eliminate HIV from an infected individual. However, the potent, complex, and active antiretroviral therapy (ART) strategies have been able to successfully inhibit HIV replication in patients. Unfortunately, obesity following ART is frequent among HIV-infected patients. The mechanism underlying ART-induced obesity is characterized based on expression of traditional markers such as genes and proteins. However, little is known about, yet another key component of molecular biology known as microRNAs (miRNAs). Micro-RNAs are ~ 22 base-long non-coding nucleotides capable of regulating more than 60% of all human protein-coding genes. The interest in miRNA molecules is increasing and their roles in HIV and obesity are beginning to be apparent. In this review, we provide an overview of HIV and its associated diseases, ART-induced obesity, and discuss the roles and plausible benefits of miRNAs in regulating obesity genes in HIV-infected patients. Understanding the roles of miRNAs in ART-induced obesity will aid in tracking the disease progression and designing beneficial therapeutic approaches.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01585-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis","authors":"Tanzeel Bashir,&nbsp;Amjad M. Husaini","doi":"10.1007/s10142-025-01592-3","DOIUrl":"10.1007/s10142-025-01592-3","url":null,"abstract":"<div><p>Horticultural crops, including fruits, vegetables, flowers, and herbs, are essential for food security and economic sustainability. Advances in biotechnology, including genetic modification and omics approaches, have significantly improved these crops'traits. While initial transgenic efforts focused on protein-coding genes, recent research highlights the crucial roles of non-coding RNAs (ncRNAs) in plant growth, development, and gene regulation. ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), influence key biological processes through transcriptional and post-transcriptional regulation. This review explores the classification, functions, and regulatory mechanisms of ncRNAs, emphasizing their potential in enhancing horticultural crop quality. This growing understanding offers promising avenues for enhancing crop performance and developing new horticultural varieties with improved traits. Additionally, we elucidate the role of ncRNA databases and predictive bioinformatics tools into modern horticultural crop improvement strategies.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143769682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico analysis of betaine aldehyde dehydrogenase (BADH) gene in different cultivars of Chenopodium quinoa","authors":"Ali Reza Mirzaei,&nbsp;Bahman Fazeli-Nasab,&nbsp;Mehrnaz Hatami,&nbsp;Ali Salehi Sardoei,&nbsp;Mansour Ghorbanpour","doi":"10.1007/s10142-025-01577-2","DOIUrl":"10.1007/s10142-025-01577-2","url":null,"abstract":"<div><p><i>Chenopodium quinoa</i> is an emerging halophyte plant that has gained significant attention from researchers in recent years due to its high nutritional value and resilience to environmental stress. This plant serves as an excellent substitute for rice and wheat. However, there has been limited research on it, leaving many of its genes still unidentified. The objective of this research was to identify gene patterns and conduct a bioinformatics analysis across various fields. The expression sequence of the <i>betaine aldehyde dehydrogenase</i> (<i>BADH</i>) gene was predicted using bioinformatics software such as PlantCARE and PlantPan. The findings indicated that different cultivars provide valuable information regarding resistance to the binding sites of MYB transcription factors, hormone response regions, and both promoter and enhancer regions, which contain 32 <i>cis</i>-regulatory elements. This emphasized the role of the <i>BADH</i> gene in responding to abiotic stress. Additionally, the research revealed that the <i>BADH</i> gene activates oxidoreductase activity across different cultivars, influencing NAD or NADP receptors that contribute to stress resistance. The protein lengths identified were 454 and 500 amino acids, respectively. Chloroplast analysis revealed that the GC content for the <i>BADH</i> gene was 37%. From this analysis, it was determined that out of 128 distinct functional genes in the genome, approximately 84 are protein-coding genes. An examination of the domains and motifs in the target genes showed that they contain two conserved sequences: Aldedh and DUF1487. Furthermore, miRNA analysis and promoter investigations indicated that the <i>BADH</i> gene plays a vital role in activating processes related to arginase, protein kinases, superoxide dismutase, tubulins, and membrane proteins. The gene is also crucial for activating nuclear transcription factors through receptor activation. In conclusion, the results suggest that <i>BADH</i> genes contribute to the plant's resistance to salt stress through various mechanisms. Stress acts as a trigger for the activation of this gene, effectively safeguarding the plant against the detrimental effects of environmental stresses.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143761819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic engineering of lipids for crop resilience and nutritional improvements towards sustainable agriculture","authors":"Swati Mangla,&nbsp;Yogesh K. Ahlawat,&nbsp;Gaurav Pathak,&nbsp;Nisha Sharma,&nbsp;Maryam Samani,&nbsp;Veer Bhan,&nbsp;Jemaa Essemine,&nbsp;Yashirdisai Sampasivam,&nbsp;Navjot Singh Brar,&nbsp;Anurag Malik,&nbsp;Vikas Ramteke,&nbsp;Shivali Gupta,&nbsp;Sumati Choubey","doi":"10.1007/s10142-025-01588-z","DOIUrl":"10.1007/s10142-025-01588-z","url":null,"abstract":"<div><p>Metabolic engineering of lipids in crops presents a promising strategy to enhance resilience against environmental stressors while improving nutritional quality. By manipulating key enzymes in lipid metabolism, introducing novel genes, and utilizing genome editing technologies, researchers have improved crop tolerance to abiotic stresses such as drought, salinity, and extreme temperatures. Additionally, modified lipid pathways contribute to resistance against biotic stresses, including pathogen attacks and pest infestations. Engineering multiple stress-resistance traits through lipid metabolism offers a holistic approach to strengthening crop resilience amid changing environmental conditions. Beyond stress tolerance, lipid engineering enhances the nutritional profile of crops by increasing beneficial lipids such as omega-3 fatty acids, vitamins, and antioxidants. This dual approach not only improves crop yield and quality but also supports global food security by ensuring sustainable agricultural production. Integrating advanced biotechnological tools with a deeper understanding of lipid biology paves the way for developing resilient, nutrient-rich crops capable of withstanding climate change and feeding a growing population.</p><h3>Graphical Abstract</h3><p>The diagram depicts how the metabolic engineering of lipids enhances crop resilience by improving stress tolerance, increases nutritional value through enrichment of essential FAs, and facilitates waste-to-energy conversion by optimizing lipid profiles for biofuel production. This integrated approach promotes sustainable agricultural practices and resource efficiency which in turn satisfies our <i>Sustainable development goals </i>viz<i>. 2,3,12, 7</i>.</p>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143740797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Emerging role and clinical applications of circular RNAs in human diseases","authors":"Subhayan Sur,&nbsp;Jayanta K. Pal,&nbsp;Soumya Shekhar,&nbsp;Palak Bafna,&nbsp;Riddhiman Bhattacharyya","doi":"10.1007/s10142-025-01575-4","DOIUrl":"10.1007/s10142-025-01575-4","url":null,"abstract":"<div><p>Circular RNAs (circRNAs) are a large family of non-coding RNAs characterized by a single-stranded, covalently closed structure, predominantly synthesized through a back-splicing mechanism. While thousands of circRNAs have been identified, only a few have been functionally characterized. Although circRNAs are less abundant than other RNA types, they exhibit exceptional stability due to their covalently closed structure and demonstrate high cell and tissue specificity. CircRNAs play a critical role in maintaining cellular homeostasis by influencing gene transcription, translation, and post-translation processes, modulating the immune system, and interacting with mRNA, miRNA, and proteins. Abnormal circRNA expression has been associated with a wide range of human diseases and various infections. Due to their remarkable stability in body fluids and tissues, emerging research suggests that circRNAs could serve as diagnostic and therapeutic biomarkers for these diseases. This review focuses on the emerging role of circRNAs in various human diseases, exploring their biogenesis, molecular functions, and potential clinical applications as diagnostic and therapeutic biomarkers with current evidence, challenges, and future perspectives. The key theme highlights the significance of circRNAs in regulating gene expression, their involvement in diseases like cancer, neurodegenerative disorders, cardiovascular diseases, and diabetes, and their potential use in translational medicine for developing novel therapeutic strategies. We also discuss recent clinical trials involving circRNAs. Thus, this review is important for both basic researchers and clinical scientists, as it provides updated insights into the role of circRNAs in human diseases, aiding further exploration and advancements in the field.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic cellular composition and immune landscape revealed by single-cell transcriptome profiling in a brain arteriovenous malformation","authors":"Yutong Liu,&nbsp;Hongchuan Niu,&nbsp;Junze Zhang,&nbsp;Rui Liang,&nbsp;Zhenyu Zhou,&nbsp;Chengxu Lei,&nbsp;Shihao He,&nbsp;Changyu Lu,&nbsp;Yuanli Zhao","doi":"10.1007/s10142-025-01590-5","DOIUrl":"10.1007/s10142-025-01590-5","url":null,"abstract":"<div><h3>Background</h3><p>Cerebral arteriovenous malformation is a congenital blood vessel abnormality with its immune mechanism remains unclear. Our study characterized the change of cellular composition and gene expression landscape in brain arteriovenous malformation (bAVM).</p><h3>Methods</h3><p>We conducted single-cell RNA sequencing analysis on one bAVM sample and three healthy control (HC) samples. Cell clustering analysis and cell type annotation were used to identify the major cell types in bAVM and HC samples. Critical differentially expressed genes between bAVM and HC sample were analyzed in each cell types to explore the functional changes of each kind of cells. We also examined the cell communication change in bAVM sample and identified the significantly changed cellular interaction pathways.</p><h3>Results</h3><p>5 major cell types were identified including NK cells, monocytes, fibroblasts, endothelial cells (EC), tissue stem cells and smooth muscle cells (SMC). In bAVM sample, proportion of monocytes raised significantly while SMC decreased. Inflammation and cell migration related genes expression and cell communication pathways changed dramatically in bAVM sample.</p><h3>Conclusion</h3><p>Inhibition of monocyte-endothelium interaction and promotion of NK cells interaction were found in bAVM sample, which may reveal a new mechanism about inflammation response and cellular impairment in the disease progression.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143707005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new perspective on endometriosis: Integrating eQTL mendelian randomization with transcriptomics and single-cell data analyses","authors":"Sheng Dou,&nbsp;Yi Wei,&nbsp;Zongyun Lin,&nbsp;Hui Wu,&nbsp;Fenglian Yang,&nbsp;Xuechang Cen,&nbsp;Wenjing Lu,&nbsp;Haimei Qin,&nbsp;Rong Wang,&nbsp;Junli Wang","doi":"10.1007/s10142-025-01543-y","DOIUrl":"10.1007/s10142-025-01543-y","url":null,"abstract":"<p>Endometriosis is caused by the migration of endometrial cells to locations outside the uterine lining. Despite the increasing prevalence of endometriosis, there has been limited research on genetic effects, and its molecular mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the development of endometriosis and to identify new genetic targets for endometriosis by integrating data from gene chips, single-cell mapping, and genome-wide association study databases. Using the Gene Expression Omnibus database, we downloaded data on normal endometrium, eutopic endometrium, and ectopic lesion tissues to explore the differentially expressed genes (DEGs) between normal and eutopic endometrium, and between eutopic and ectopic endometrium. Assessment of the relationships between DEGs and endometriosis involved differential expression, expression quantitative trait loci (eQTL), and Mendelian randomization (MR) analyses. Two single-cell atlas datasets were then analyzed to explore the mechanisms underlying disease development and progression. Intersection of MR results with DEGs between normal and eutopic endometrium highlighted 28 candidate biomarker genes (17 upregulated and 11 downregulated). Similarly, we identified two additional candidate biomarker genes by intersecting the DEGs between eutopic and ectopic endometrium with MR results. Among these 30 candidates, further filtering using single-cell datasets revealed that the histamine N-methyltransferase (<i>HNMT</i>), coiled-coil domain containing 28 A (<i>CCDC28A</i>), fatty acid desaturase 1 (<i>FADS1</i>) and mahogunin ring finger 1 (<i>MGRN1</i>) genes were differentially expressed between the normal and eutopic groups, consistent with transcriptomic and MR results. Our findings suggested that eutopic endometrium exhibits epithelial-mesenchymal transition (EMT). Cell communication analysis focused on ciliated epithelial cells expressing <i>CDH1</i> and <i>KRT23</i> revealed that, in the eutopic endometrium, ciliated epithelial cells are strongly correlated and interact with natural killer cells, T cells, and B cells. We identified four novel biomarker genes and found evidence for EMT in the eutopic endometrium. The mechanism of endometriosis progression may be closely related to EMT and changes in the immune microenvironment triggered by damage to ciliated epithelial cells.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10142-025-01543-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143706912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of the STY13 gene family across the entire genome and an analysis of the essential function of GhSTY13-12 in cotton’s response to abiotic stress","authors":"Shaoliang Zhang,&nbsp;Huiyun Shan,&nbsp;Xiaopei Bo,&nbsp;Jiahui Li,&nbsp;Zili Liu,&nbsp;Pengtao Li,&nbsp;Yuling Liu,&nbsp;Xiaojie Yang,&nbsp;Quanwei Lu,&nbsp;Sumei Wan,&nbsp;Renhai Peng,&nbsp;Yangyang Wei,&nbsp;Shoulin Hu","doi":"10.1007/s10142-025-01570-9","DOIUrl":"10.1007/s10142-025-01570-9","url":null,"abstract":"<div><p>Cotton is an important cash crop, and its yield and quality were affected by abiotic stresses. The serine/threonine protein kinase <i>STY13</i> gene, belonging to the protein kinase family, is one of the largest and most functionally diverse gene families, which is a critical regulatory molecule for cell function. In this study, we systematically identified and analyzed the <i>STY13</i> gene family in two major cultivated cotton species (<i>Gossypium hirsutum</i> and <i>Gossypium barbadense</i>) and their two ancestors (<i>Gossypium arboretum</i> and <i>Gossypium raimondii</i>). A total of 46, 50, 26 and 24 <i>STY13</i> genes were identified from these four species, respectively. Phylogeny analysis showed that cotton <i>STY13</i> genes (cotton STY protein kinase genes) could be classified into five groups. This gene family was evenly distributed on each chromosome in cotton. <i>STY13</i> genes contain light-responsive elements, stress-responsive elements, growth and developmental elements, and multiple gene and protein binding sites. Most motifs in the <i>STY13</i> proteins were conserved and had similar distribution patterns. However, there were some differences in specific motifs in different subfamilies. Gene expression analysis based on RNA-seq and qRT-PCR showed that <i>STY13</i> genes were responsive to abiotic stress. <i>GhSTY13-12</i> gene was located in cytoplasm. Silencing of the <i>GhSTY13-12</i> gene resulted in reduced leaf chlorosis, increased total antioxidant capacity, decreased malondialdehyde content, and enhanced drought and salt tolerance. These results provide a scientific basis for further research on the function of <i>STY13</i> in cotton and its application on cotton trait improvement.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143698657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cutting edge: ferroptosis in metabolic dysfunction-associated steatotic liver disease (MASLD) pathogenesis and therapy","authors":"Amr Ali Mohamed Abdelgawwad El-Sehrawy,&nbsp;Teeba Ammar Rashid,&nbsp;Muhammad Ikram Ullah,&nbsp;Subasini Uthirapathy,&nbsp;Subbulakshmi Ganesan,&nbsp;Abhayveer Singh,&nbsp;Anita Devi,&nbsp;Kamal Kant Joshi,&nbsp;Ahmed Salman Jasim,&nbsp;Abed J. Kadhim","doi":"10.1007/s10142-025-01579-0","DOIUrl":"10.1007/s10142-025-01579-0","url":null,"abstract":"<div><p>Ferroptosis denotes a distinct form of controlled cell death marked by substantial iron buildup and significant lipid peroxidation, playing a crucial role in several disease processes linked to cell death. Given the liver's essential functions in iron and lipid metabolism and its vulnerability to oxidative damage, more research has investigated the correlation between ferroptosis and numerous hepatic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease (NAFLD). NAFLD has arisen as a worldwide public health concern due to elevated morbidity and high death rates. The pathogenesis of MASLD remains incompletely elucidated. Recent data suggests that ferroptosis is crucial in the pathophysiology of MASLD; nevertheless, the specific processes by which ferroptosis influences MASLD remain unclear. The present review summarizes the molecular processes of ferroptosis and its intricate regulatory networks, outlines the differing impacts of ferroptosis at different stages of MASLD, and examines possible approaches targeting ferroptosis for the therapy of MASLD, suggesting a novel approach for its management.</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143688523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive study of tRNA-derived fragments in plants for biotic stress responses","authors":"Supriya P. Swain,&nbsp;Niyati Bisht,&nbsp;Shailesh Kumar","doi":"10.1007/s10142-025-01576-3","DOIUrl":"10.1007/s10142-025-01576-3","url":null,"abstract":"<div><p>Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. <i>Arabidopsis thaliana, Oryza sativa,</i> and <i>Solanum lycopersicum</i> are investigated using <i>in-silico</i> approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study’s database is publicly available at http://www.nipgr.ac.in/PbtRFdb.\u0000</p></div>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143688525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}