BMC Genomics最新文献

{"title":"Mechanisms underlying the estradiol mediated protection of yak oviduct epithelial cells against ER-Ca²⁺ imbalance.","authors":"Xiaolin Ye, Meng Wang, Yangyang Pan, Tianhao Li, Jinglei Wang, Ling Zhao, Rui Zhang, Yan Cui, Sijiu Yu","doi":"10.1186/s12864-025-11804-6","DOIUrl":"10.1186/s12864-025-11804-6","url":null,"abstract":"<p><strong>Background: </strong>Extreme weather events are occurring with increasing frequency worldwide. Oviduct epithelial cells (OECs), which provide nutrients and a microenvironment critical for reproductive processes such as fertilization and early embryonic development, are vulnerable to extreme hyperthermia climate. Mitigating heat induced damage to yak oviduct epithelial cells (YOECs) may thus contribute to improving reproductive health. Studies have shown that hyperthermia reduces SERCA protein levels, leading to ER-Ca²⁺ dyschondrosteosis and subsequent cellular injury; this phenomenon indicates that ER-Ca imbalance is a critical factor in cellular damage. Estradiol (E₂), which not only promotes the YOEC functions essential for fertilization and early embryonic development but also participates in calcium regulation, is hypothesized to alleviate ER-Ca²⁺ imbalance induced YOEC damage. To test this hypothesis, we compared the ER-Ca²⁺ distribution and hyperthermia/ hapsigargin (TG, a SERCA inhibitor)-mediated cellular damage in YOECs under high temperature conditions. Proteomic sequencing was employed to analyze protein level changes in TG treated YOECs with ER-Ca²⁺ imbalance before and after E₂ treatment, elucidating the mechanism whereby E₂ mitigates YOEC injury.</p><p><strong>Results: </strong>E₂ can alleviate the damage in YOECs caused by TG. This effect is associated with perturbations in the restored serine 927 phosphorylation site in type 3 inositol 1,4,5-trisphosphate receptor (IP3R3). Restoration of the serine 927 phosphorylation site in IP3R3 leads to an increase in ER-Ca²⁺ levels, which activates the calmodulin phosphatase/nuclear factor of the activated T cells pathway and promotes cell function, and reduces YOECs apoptosis under ER-Ca²⁺ conditions.</p><p><strong>Conclusion: </strong>Our research results indicate that E₂ protects YOECs under ER-Ca²⁺ imbalance by increasing the protein expression of IP3R3 serine 927, highlighting the close relationship between protein expression and phosphorylation modification during ER-Ca²⁺ imbalance. These findings deepen our understanding of ER-Ca²⁺ imbalance damage and lay the foundation for further research and mitigation of related diseases.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"613"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of NUDIX enzymes across fungi reveals previously unrecognized diversity.","authors":"Zofia Pasterny, Drishtee Barua, Eugenio Mancera, Anna Muszewska","doi":"10.1186/s12864-025-11778-5","DOIUrl":"10.1186/s12864-025-11778-5","url":null,"abstract":"<p><strong>Background: </strong>The NUDIX superfamily encompasses highly diverse enzymes involved in a plethora of biological functions such as mRNA metabolism, DNA repair, and lipid peroxidation. These hydrolases are found in all domains of life and show surprising versatility in terms of the substrates that they process. The knowledge about the diversity of fungal NUDIX proteins is fragmentary, being largely limited to a small number of characterized enzymes from yeasts. To address this knowledge gap systematically, we performed a detailed analysis of the NUDIX hydrolases across 183 fungal proteomes.</p><p><strong>Results: </strong>Members of six of the known NUDIX families were present in fungi being particularly abundant in Glomeromycota. Phylogenetic analysis and sequence clustering grouped fungal NUDIX enzymes in 25 subfamilies, 13 of which did not cluster with previously known enzymes. These 13 newly identified subfamilies all belong to the canonical NUDIX family, and structural comparison revealed a typical NUDIX fold with α-β-α sandwich structure. Molecular docking suggested Ap3A and Ap4A as substrates with the highest binding affinity, but their possible cellular roles remain unclear. We also found evidence of expression of most of the genes that encode these enzymes, suggesting physiological relevance.</p><p><strong>Conclusions: </strong>Our analysis offers a comprehensive perspective on the structural and sequence relationships of the NUDIX superfamily across fungi with potential to guide experimental characterization of their biological functions.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"606"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and functional insights into commensal streptococci with anti-pneumococcal activity.","authors":"Sara Handem, Bárbara Ferreira, Carina Valente, Raquel Sá-Leão","doi":"10.1186/s12864-025-11756-x","DOIUrl":"10.1186/s12864-025-11756-x","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"577"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide characterization of monoacylglycerol lipase (MAGL) gene family in soybean and functional analysis of GmMAGLs in storage lipid metabolism and drought resistance.","authors":"Haiqing Jing, Yan Sun, Bicheng Wang, Juhua Ma, Kun Wan, Zhanqian Li, Yali Zhou, Runzhi Li, Haiping Zhang, Jinai Xue","doi":"10.1186/s12864-025-11813-5","DOIUrl":"10.1186/s12864-025-11813-5","url":null,"abstract":"<p><strong>Background: </strong>Monoglyceride lipase (MAGL) catalyzes the final step of triacylglycerol (TAG) hydrolysis, converting monoacylglycerol (MAG) into glycerol and free fatty acids. Although MAGL is critical for TAG metabolism, its physiological roles in plants remain poorly understood, compared to its functions in mammals.</p><p><strong>Results: </strong>Eighteen GmMAGL genes were identified from the genome of soybean (Glycine max), a major food and oil crop worldwide, with them being classified into 8 distinct subfamilies. Collinearity analysis indicated that segmental duplication was the only force driving GmMAGL gene family expansion. Multiple sequence alignment demonstrated that all 18 GmMAGLs harbored two typical structural features: the lipase GXSXG (Gly-X-Ser-X-Gly) motif and the catalytic triad consisting of Ser, Asp and His residues. Notably, GmMAGL14 and GmMAGL15 harbored an additional acyltransferase motif, distinguishing them as the only two bifunctional enzymes (hydrolase and acyltransferase) within the GmMAGL family. Additionally, multiple cis-elements associated with development, hormone, and stress response were identified in the promoter regions of GmMAGL genes. RNA-seq data revealed that GmMAGL genes displayed tissue-specific or distinct expression patterns in response to abiotic stresses and hormone treatments. Remarkably, the expression of GmMAGL10 and 14 was negatively related to oil accumulation during seed development while GmMAGL3 exhibited high expressions during seed germination. Particularly, 6 GmMAGL genes (GmMAGL1/3/4/6/8/12) showed significant modulation in response to drought stress in roots and leaves of soybean seedlings.</p><p><strong>Conclusions: </strong>This study represents the first comprehensive identification of 18 members of GmMAGL gene family in soybean. GmMAGL10 and 14 may impact seed oil content negatively while GmMAGL3 function importantly in seed germination. GmMAGL1/3/4/6/8/12 might confer drought tolerance by activating lipid metabolism in soybean seedlings. The present data establish a foundation for further elucidation of the biological functions of GmMAGL genes and provide valuable target genes for genetic improvement in soybean and other crops.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"625"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and characterization of the CCT gene family in Chinese cabbage (Brassica rapa) response to abiotic stress.","authors":"Haoqi Liu, Zhiyuan Yin, Mengping Qiu, Yan Yang, Ye Xu, Han Wang, Min Yan, Guohua Xu","doi":"10.1186/s12864-025-11768-7","DOIUrl":"10.1186/s12864-025-11768-7","url":null,"abstract":"<p><strong>Background: </strong>The CCT (CONSTANS, CONSTANS-LIKE and TOC1) gene family plays a crucial role in regulating diurnal rhythms and responding to abiotic stress, which significantly impacts crop growth, development, and yield. However, comprehensive information on the CCT gene family in Chinese cabbage (Brassica rapa) is currently unavailable.</p><p><strong>Results: </strong>In this study, we conducted a genome-wide identification and analysis ofCCT genes in Chinese cabbage. In total, we identified 66 CCT genes in the Chinese cabbage genome, and we elucidated the physicochemical properties and subcellular locations of the corresponding CCT proteins. Phylogenetic analysis, examination of conserved motifs, and gene structure analysis revealed that the BraCCT gene family could be classified into three well-conserved subfamilies: COL, PRR, and CMF. The BraCCT gene family has close relationships with Arabidopsis thaliana. Sixty-three pairs of BraCCTs exhibited collinear relationships through interchromosomal synteny analysis in Brassica rapa, indicating that segmental duplication played a vital role in the expansion of the BraCCT gene family. Cis-acting elements of the CCT promoters have been identified to play a role in plant development, hormonal responses, and stress responses. Expression profile analysis showed that CCT genes were extensively expressed in various tissues of Chinese cabbage, exhibiting diverse expression patterns appeared to be diverse. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of ten CCT genes confirmed their response to heat stress, cold stress, drought stress, and abscisic acid stress. The full-length coding sequence of BraCCT24 was obtained using homologous cloning technology, and further investigation revealed that the BraCCT24 protein is located in the nucleus.</p><p><strong>Conclusions: </strong>In this study, 66 CCT genes were identified in Brassica rapa, and their phylogenetic relationships, gene structural features, duplication events, gene expression, and potential roles in Brassica rapa development were investigated. Overall, this study offers a theoretical foundation for further investigating the significant role of the CCT gene family in the functional genome of Chinese cabbage.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"593"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA binding protein HuR regulated by OIP5-AS1 may be involved in maternal transcript degradation during the human maternal-to-zygotic transition.","authors":"Yan-Na Liu, Ke-Yi Li, Hao Wei, Wen-Xiu Li, Yue-Hua Zhang, Jia-Jun Qiu, Fanyi Zeng, Jing-Bin Yan","doi":"10.1186/s12864-025-11807-3","DOIUrl":"10.1186/s12864-025-11807-3","url":null,"abstract":"<p><strong>Background: </strong>The maternal-to-zygotic transition (MZT) is a critical process in early human development, involving the degradation of maternal gene transcripts and activation of zygotic genes. Any disruption in the degradation of maternal transcripts may be associated with some reproductive disorders. However, the precise mechanism by which maternal gene transcripts are degraded during this transition remains unclear.</p><p><strong>Results: </strong>Through an analysis of weighted gene co-expression networks, an oocyte-specific module was identified, showing high consistency with the expression pattern of maternal transcripts degraded at the 8-cell stage, which is associated with the cell cycle and transcription factor binding. Within this module, a maternal long non-coding RNA known as OIP5 antisense RNA 1 (OIP5-AS1) was identified. It was observed that OIP5-AS1 can bind to the RNA binding protein human antigen R (HuR), potentially limiting its availability for other mRNAs and contributing to the degradation of maternal transcripts during MZT. Moreover, RNA immunoprecipitation sequencing in human induced pluripotent stem cells (iPSCs) revealed HuR and OIP5-AS1 are likely to tightly bind together and involved in functions related to the cell cycle and transcriptional regulation. Upon knocking down OIP5-AS1 and the ELAVL1 gene, which encodes the HuR protein in human iPSCs, a significant reduction in the expression levels of maternal transcripts was observed, suggesting an essential role of these factors in regulating maternal transcript stability during early development.</p><p><strong>Conclusions: </strong>The HuR protein plays a critical role in influencing the degradation of maternal transcripts during the MZT in early human embryonic development. Understanding the role of OIP5-AS1 in regulating HuR protein could provide valuable insights into developmental biology and potentially lead to new therapeutic strategies for developmental disorders.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"600"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic surveillance reveals geographical heterogeneity and differences in known and novel insecticide resistance mechanisms in Anopheles arabiensis across Kenya.","authors":"Brian Polo, Kelly L Bennett, Sonia Barasa, Jon Brenas, Silas Agumba, Joseph Mwangangi, Lucy Wachira, Stanley Kitur, Damaris Matoke-Muhia, David M Mburu, Edith Ramaita, Elijah O Juma, Charles Mbogo, Eric Ochomo, Chris S Clarkson, Alistair Miles, Luna Kamau","doi":"10.1186/s12864-025-11788-3","DOIUrl":"10.1186/s12864-025-11788-3","url":null,"abstract":"<p><strong>Background: </strong>Insecticide resistance in disease vectors poses a significant threat to the control of transmission globally. In Anopheles mosquitoes, resistance has jeopardized gains made in malaria control and led to the resurgence of cases. Although Anopheles arabiensis is a major malaria vector, little is known about its genetic diversity and insecticide resistance mechanisms across geographical space. There is an urgent need to incorporate genomics in resistance monitoring to allow preemptive detection of adaptive alleles.</p><p><strong>Methods: </strong>We analyzed whole-genome data from 498 An. arabiensis specimens collected across five regions in Kenya. Population structure was assessed and both known and novel resistance mechanisms were investigated through SNP and CNV frequency analysis, genome-wide selection scans and haplotype clustering.</p><p><strong>Results: </strong>Analyses of whole-genome data revealed geographical population structure between the northwestern region and central coastal Kenya, which was likely influenced by the Great Rift Valley. Distinct geographical differences in insecticide resistance profiles were observed across Kenya, reflecting differences in ecology, land use and selection pressure. For instance, in central Kenya, copy number variants at the Cyp6aa/p gene cluster and carboxylesterase genes associated with metabolic resistance to pyrethroids and organophosphates are fixed. In contrast, northwestern Kenya had mutations associated with both the target site and metabolic resistance to pyrethroids and DDT at high frequencies. Vgsc-L995F mutations occurred at frequencies of up to 44%, and duplications of Cyp9k1 occurred at frequencies of up to 66%. Genome-wide selection scans identified novel candidates under selection in central Kenya, including the Keap1 gene, which is involved in the regulation of multiple detoxification genes, likely due to high insecticide pressure in the region.</p><p><strong>Conclusion: </strong>Restricted gene flow coupled with heterogeneity in molecular insecticide resistance across Kenya suggests that localized control measures may be more effective in preventing the spread of insecticide resistance in An. arabiensis. This study highlights the importance of incorporating genomics in the routine monitoring of malaria vector populations to identify the emergence of new resistance signatures and their geographic distribution and spread.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"599"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune response of intestinal micrornas to transport stress in hybrid yellow catfish (tachysurus fulvidraco♀ ×t. vachellii♂) : response strategy and potential biomarker.","authors":"Tao Zheng, Yifan Tao, Siqi Lu, Jun Qiang, Pao Xu","doi":"10.1186/s12864-025-11757-w","DOIUrl":"10.1186/s12864-025-11757-w","url":null,"abstract":"<p><p>Fish transportation, a routine operation in aquaculture, can induce immune responses in fish, potentially affecting their health. Nevertheless, the immune response mechanisms involved in microRNAs (miRNAs) under transport stress remain unclear. Therefore, we investigated the immune response strategy of miRNAs in intestines of hybrid yellow catfish under transport stress via physiological, biochemical and RNA-seq analysis. We found that transportation induced innate immune response of intestines characterized by significant increases in alkaline phosphatase, acid phosphatase, lysozyme, and complement 3 level. Meanwhile, 50 differentially expressed miRNAs were identified and comprehensive analysis of miRNA-mRNA sequencing showed their targets genes involved in 9 immune-related pathways. Notably, the miRNAs involved in immune regulation, such as miR-29a/b, miR-106, miR-454-3p and miR-455, were notably upregulated following the induction of transport stress, while miR-196a-5p was significantly downregulated. In addition, their corresponding target genes such as tkt, mafg, arap2, nfatc2, egr2 and wnk4 showed opposite expression trends, suggesting that these genes may be the key immunomodulatory targets of corresponding miRNA. Here, we focused on the regulatory function of miR-455 and its predictive target genes egr2. Double luciferase assay revealed that miR-455 might exist binding site in the 3'-UTR sequence of egr2 mRNA. Interestingly, silencing miR-455 under transport stress led to the increase of intestinal egr2 expression, affected intestinal immune and inflammation responses, and caused intestinal tissue damage and abnormal secretion of mucous substances. In conclusion, transport stress triggered intestinal immune response, and multiple miRNAs played important role in immune response, among which miR-455 might be an important biomarker. These findings not only improve the understanding of the immunomodulatory function of miRNA in fish, but also provide a theoretical basis for screening potential regulatory targets under transport stress.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"582"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and stress-responsive expression profiling of the TCP gene family in Cenchrus fungigraminus under drought and cold stress.","authors":"Shijie Ke, Xin He, Mengmeng Zhang, Lin Luo, Yuxin Chen, Yixue Cui, Yelin Huang","doi":"10.1186/s12864-025-11798-1","DOIUrl":"10.1186/s12864-025-11798-1","url":null,"abstract":"","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"626"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection of reference genes in Thermothelomyces fergusii: insights from genomic and expression analysis in response to different carbon sources.","authors":"Abdul Waheed, Yi Chen, Hafiz Muhammad Rizwan, Muhammad Adnan, Xuekun Ma, Gang Liu","doi":"10.1186/s12864-025-11772-x","DOIUrl":"10.1186/s12864-025-11772-x","url":null,"abstract":"<p><strong>Background: </strong>RNA expression analysis using reverse transcription qPCR requires reference genes for accurate data normalization. However, some reference genes can show significant variability in specific biological samples, raising concerns about the reliability of this method. This study assessed the expression levels of 12 reference genes in Thermothelomyces fergusii during spore and mycelium cultivation under different carbon source media (avicel, cellobiose, and glucose) using RT-qPCR. T. fergusii is a thermophilic fungus known for its abundance of cellulase and industrial applications. Quantifying fungal gene expression using the RT-qPCR method is essential for investigating the molecular biology of T. fergusii.</p><p><strong>Results: </strong>The stability of 12 reference genes in T. fergusii was evaluated using RefFinder, geNorm, NormFinder, BestKeeper, and delta Ct techniques. The robustness of the chosen reference gene was verified using the LPMO AA9-4 gene. Analysis of the different methods showed variations in the results of reference genes under different sugar treatments. Consistently, EF1, GAPDH, and 18 S-3 were identified as reliable reference genes by the geometric mean of ranking values from Pearson correlation coefficient (r) analysis of pooled data, ranking values of RefFinder in pooled data, and NormFinder of pooled data. However, BT-3, ACT-3, and 18 S-2 exhibited inconsistency as reference genes.</p><p><strong>Conclusion: </strong>These results emphasize the importance of verifying reference genes in specific experimental models and provide valuable recommendations for selecting reliable reference genes in RT-qPCR. These findings have broad applicability for gene expression investigations involving T. fergusii.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"586"},"PeriodicalIF":3.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144538417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}