Genes最新文献

{"title":"Type I Interferon Emerges as the Reproducible Core of a Shared Mitochondrial-Immune Transcriptomic Signature in Pulmonary Arterial Hypertension and Bipolar Disorder.","authors":"Cristina Ioana Stoica, Cătălin Araniciu, Ioana Andrada Ionuț, Anca Stana, Smaranda Dafina Oniga","doi":"10.3390/genes17091147","DOIUrl":"10.3390/genes17091147","url":null,"abstract":"<p><p><b>Background/Objectives:</b> Mitochondrial dysfunction and immune activation are reported across many chronic diseases, yet whether such shared signals are reproducible across independent cohorts is rarely tested. We compared the peripheral blood transcriptomes of two clinically distinct disorders, pulmonary arterial hypertension (PAH) and bipolar disorder (BD), to determine which shared transcriptomic signals remain directionally concordant across independent cohorts. <b>Methods</b>: Five public microarray cohorts (two PAH, three BD) were analyzed through differential expression, Hallmark gene set enrichment, and weighted gene co-expression network analysis. Instead of focusing on overlapping genes, we quantified the directional reproducibility of pathway-level signals using a stability index, evaluated against chance baselines, permutation testing, and complementary reproducibility metrics. <b>Results</b>: Both disorders converged on an overlapping mitochondrial-immune transcriptional program, and the interferon-α response was the only Hallmark pathway with positive normalized enrichment score (NES) values across all five cohorts and was significantly enriched in four of them. Beyond the interferon response, the broader pathway signature was directionally concordant across the two PAH cohorts (stability index = 0.66; Spearman ρ = 0.61) but not across the three BD cohorts (0.22; ρ = 0.14). <b>Conclusions</b>: PAH and BD share a peripheral mitochondrial-immune transcriptional program whose most reproducible element is type I interferon signaling, a signal directionally preserved across all cohorts despite differences in blood fraction. The broader transcriptomic program showed variable reproducibility that depended in part on the blood fraction sampled, highlighting the importance of evaluating both reproducibility and sample characteristics before inferring shared disease biology.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding MAPT Exon 10 Mis-Splicing in FTDP-17: From Pathogenic Mechanisms and Experimental Models to Molecular Therapies.","authors":"Giuseppina Covello","doi":"10.3390/genes17091150","DOIUrl":"10.3390/genes17091150","url":null,"abstract":"<p><p>Frontotemporal Dementia and Parkinsonism linked to chromosome 17 (FTDP-17) is a rare, early-onset, autosomal-dominant neurodegenerative tauopathy caused by mutations in the <i>Microtubule-Associated Protein Tau</i> (<i>MAPT</i>) gene. A subset of these mutations selectively disrupts the normal alternative splicing of MAPT exon 10, altering the physiological ratio of 3-Repeat (3R) and 4-Repeat (4R) tau isoforms; this imbalance, driving pathological tau aggregation and progressive neurodegeneration, is a pathogenic hallmark of FTDP-17. This review explores the molecular mechanisms regulating exon 10 splicing, focusing on how exonic and intronic splicing mutations destabilise mRNA structures or alter splicing factor binding, and discusses how these changes can cause disease symptoms in experimental models. It describes different research methods for studying splicing issues, including minigene reporters, cell lines, human induced pluripotent stem cell (iPSC)-derived neurons, brain organoids and mouse models that naturally express only 4R tau. It also covers potential therapeutic approaches applicable to restoring the normal 3R/4R tau ratio. These include Antisense Oligonucleotides (ASOs), RNA interference (siRNA), Small-Molecule Splicing modulators (SMCs), Spliceosome-Mediated RNA <i>trans</i>-splicing (SMaRT), CRISPR-based transcript engineering, genome editing and RNA stem-loop binders. Additionally, the review highlights recent Phase 2 trial results, including the Diranersen (BIIB080) tau-lowering ASO, the development of MAPT-targeted RNA therapies, new tau-PET and plasma p-tau biomarkers, and innovative strategies to deliver CNS treatments, including non-invasive approaches. By integrating advances in RNA biology, disease modelling and targeted therapies, the review outlines potential future strategies for treating FTDP-17 and other tau-related disorders.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of Candidate Urinary microRNAs in Upper Tract Urothelial Carcinoma: A Prospective Multicenter Biomarker Study (JCOG1403A1).","authors":"Shuichi Tatarano, Hideki Enokida, Hiroyuki Nishiyama, Takahiro Kojima, Hirofumi Yoshino, Takahiko Mitsui, Akihiro Ito, Tomonori Habuchi, Keisuke Kanato, Hiroshi Kitamura","doi":"10.3390/genes17091145","DOIUrl":"10.3390/genes17091145","url":null,"abstract":"<p><strong>Objectives: </strong>To evaluate the clinical associations of candidate urinary microRNAs (miRNAs) in patients with upper tract urothelial carcinoma (UTUC), including their ability to discriminate patients with UTUC from healthy controls and their associations with relapse-free survival (RFS).</p><p><strong>Methods: </strong>This prospective multicenter ancillary study of the JCOG1403 trial (JCOG1403A1 study) included 45 patients with UTUC and 16 healthy controls. Four candidate miRNAs (miR-130b, miR-182, miR-191, and miR-200a) were selected based on prior exploratory sequencing analysis. Urinary cell fractions were isolated by cell sorting, and miRNA expression was quantified by stem-loop RT-qPCR. The ability of urinary miRNAs to discriminate patients with UTUC from healthy controls, their associations with clinicopathological characteristics, and their associations with RFS were evaluated.</p><p><strong>Results: </strong>Among the candidate miRNAs, miR-191 and miR-200a showed significantly increased expression in patients with UTUC and demonstrated favorable discrimination between patients with UTUC and healthy controls. The combined miR-191/miR-200a model showed the highest discriminatory performance (area under the curve, 0.888). Urine cytology was positive in 33.3% of evaluable patients, whereas urinary miR-191 and miR-200a were detectable in 78.6% and 85.7% of patients with negative/suspicious cytology, respectively. Preoperative urinary miR-182 and miR-191 detectability was significantly associated with pathological tumor stage. In exploratory prognostic analyses, patients with detectable postoperative urinary miR-130b had significantly shorter RFS (log-rank <i>p</i> = 0.0455)<b>;</b> however, the association was not statistically significant in multivariable Cox regression analysis (hazard ratio 2.76, 95% confidence interval 0.84-9.05, <i>p</i> = 0.094).</p><p><strong>Conclusions: </strong>Urinary miR-191 and miR-200a showed potential for discriminating patients with UTUC from healthy controls and may complement urine cytology, particularly in patients with negative/suspicious cytology. The association between postoperative urinary miR-130b detectability and RFS should be considered exploratory and requires further validation.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-Cell Transcriptomic Profiling of Peripheral Blood in a Patient with Progressive Thyroid Eye Disease Following Total Thyroidectomy.","authors":"Ainura Mussakulova, Zarina Zhalgasbaeva, Vyacheslav Korobeynikov, Gulnur Zhunussova","doi":"10.3390/genes17091143","DOIUrl":"10.3390/genes17091143","url":null,"abstract":"<p><p>Thyroid eye disease (TED) is an autoimmune inflammatory disorder of the orbit closely associated with thyroid dysfunction. Total thyroidectomy is traditionally expected to attenuate the autoimmune cascade, yet some patients continue to progress after surgery, which challenges this paradigm and points to a potentially autonomous orbital immune response. To investigate this, we performed single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from a 47-year-old woman with severe, glucocorticoid-refractory TED, four years after total thyroidectomy, and compared her immune landscape with that of an age- and sex-matched healthy control. The patient's peripheral blood showed a clear shift toward an active, stress-associated inflammatory state: pro-inflammatory mediators, immediate-early response transcription factors (<i>FOS</i>, <i>JUNB</i>, <i>FOSB</i>, <i>TNFAIP3</i>), and survival-related genes (<i>CXCR4</i>, <i>DDIT4</i>) were all upregulated. Gene Set Enrichment Analysis (GSEA) pointed to different mechanisms across cell types-myeloid cells were enriched for IL-6/JAK/STAT3 and TNF-α signaling, activated T cells for oxidative phosphorylation and mTORC1 signaling-while B lymphocytes and NK cells showed the opposite pattern, with reduced inflammatory and metabolic activity. One possible explanation is a \"tissue-drainage\" effect, where the most pathogenic lymphocytes leave the bloodstream and migrate into the inflamed orbital tissue along chemokine gradients. Together, these findings point to the <i>CXCR4</i>/<i>CXCL12</i> axis and cellular stress pathways as candidate therapeutic targets, though as a single-case observation this remains preliminary and requires validation in larger cohorts, at the protein level, and in functional in vitro/in vivo studies.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 of bHLH Transcription Factors and Screening of Candidate Regulators Associated with Flavonoid Biosynthesis in <i>Platycodon grandiflorus</i> Under Methyl Jasmonate Treatment.","authors":"Yalan Feng, Runlong Wei, Yeying Wu, Dandan Cheng, Zhao Zhao, Chao Ma","doi":"10.3390/genes17091144","DOIUrl":"10.3390/genes17091144","url":null,"abstract":"<p><p><b>Background</b>: The bHLH transcription factor family plays crucial roles in plant secondary metabolism, yet its genome-wide characterization and regulatory functions in flavonoid biosynthesis remain unexplored in <i>Platycodon grandiflorus</i>, a medicinal species with bioactive flavonoids. This study aims to systematically identify <i>PgbHLH</i> genes and screen for candidate regulators of flavonoid production. <b>Methods</b>: We performed genome-wide identification of bHLH family members using curated reference genomes, followed by phylogenetic classification, chromosomal localization, gene structure analysis, and collinearity assessment. Promoter cis-element prediction and subcellular localization assays for selected proteins were conducted. Expression profiles under methyl jasmonate (MeJA) treatment were evaluated via transcriptome sequencing and RT-qPCR. Protein-protein interaction prediction, expression correlation, and weighted gene co-expression network analysis (WGCNA) were integrated to link <i>PgbHLH</i> genes with flavonoid structural genes. <b>Results</b>: A total of 95 <i>PgbHLH</i> genes were identified and clustered into 23 subfamilies, unevenly distributed across nine chromosomes. All members retained conserved bHLH domains but varied in exon-intron structures. Thirty-six duplication events were detected, with Ka/Ks ratios indicating purifying selection. Promoters harbored multiple hormone- and stress-responsive elements. PgbHLH37, PgbHLH42, and PgbHLH70 were confirmed to be nuclear-localized. Transcriptomic and RT-qPCR data showed differential expression of <i>PgbHLH</i> genes in response to MeJA. Integrative analyses identified 23 PgbHLH members associated with flavonoid biosynthetic genes, among which PgbHLH37, PgbHLH42, and PgbHLH70 exhibited strong multi-dimensional correlations and were nominated as high-priority candidate regulators. <b>Conclusions</b>: This systematic characterization provides a foundation for understanding bHLH-mediated flavonoid metabolism in <i>P. grandiflorus</i>, with three prioritized candidates for future functional validation. The findings are strictly supported by the presented genomic and expression evidence. However, our conclusions are based on total flavonoid content, and analysis of individual flavonoid species is required to determine pathway-specific regulation.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of a Highly Efficient and Chemically Inducible Gene Expression System.","authors":"Yizhong Zhang, Linqiong Deng, Qing Li, Likun Lian","doi":"10.3390/genes17091142","DOIUrl":"10.3390/genes17091142","url":null,"abstract":"<p><strong>Background: </strong>Chemically inducible gene expression systems provide precise control over the temporal and spatial expression of genes. They are powerful tools for analyzing gene function during plant development and can effectively avoid the issues associated with transgene expression driven by constitutive promoters. The <i>alc</i> gene expression system derived from <i>Aspergillus nidulans</i> is one of the most promising chemically inducible expression systems in plants, owing to its significant potential for both basic research and agricultural applications. Previous studies have demonstrated the utility of the <i>alc</i> system in several dicot species, but systematic optimisation of promoter architecture and induction methodology in <i>Arabidopsis</i> remains comparatively limited.</p><p><strong>Methods: </strong>We employed a multi-level study design, combining <i>Agrobacterium</i>-mediated genetic transformation, GUS histochemical staining, and GUS quantitative assays. First, different types of <i>alc</i> gene expression systems were constructed through codon optimization of the <i>GUS</i> and <i>alcR</i> genes, and by incorporating the CaMV 35S minimal promoter (min35S), the TMV omega sequence, the Kozak sequence, and specific binding sites for the AlcR transcription factor. Second, these distinct <i>alc</i> expression systems were individually transformed into <i>Arabidopsis thaliana</i> to obtain single T-DNA insertion homozygous transgenic plants. Third, ethanol was applied via root drench, foliar spray, or vapor induction, and the performance of different <i>alc</i> systems was evaluated based on GUS protein expression, to determine the optimal induction conditions and identify the most efficient ethanol-inducible gene expression system.</p><p><strong>Results: </strong>Four <i>alc</i> systems (Ves1-Ves4) were successfully developed. <i>GUS</i> gene expression driven by these systems was precisely regulated by ethanol and was dependent on induction time and the method of induction. Among the induction methods, ethanol vapor was the most effective, followed by root drench, whereas foliar spray was the least effective. Furthermore, Ves1 was identified as the most efficient <i>alc</i> expression system, Ves2 as an efficient <i>alc</i> expression system, Ves3 as a usable <i>alc</i> expression system, and Ves4 as potentially defective with limited practical application value.</p><p><strong>Conclusions: </strong>This work lays a foundation for further research on the efficient <i>alc</i> system and the exploration of its molecular mechanism underlying high expression efficiency. The most efficient Ves1 and the highly efficient Ves2 provide a clear basis for selection in subsequent applied research, and they are expected to play a greater role in plant functional genomics and agricultural biotechnology.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Significance of Somatic Variants Involved in the Development of Pancreatic Cancer in Patients with HBOC-Associated Germline Variants.","authors":"Koki Uchiyama, Hinano Nishikubo, Tomoya Sano, Yukina Furukawa, Dongheng Ma, Daiki Imanishi, Takemi Ishidate, Hongdong Gao, Canfeng Fan, Masakazu Yashiro","doi":"10.3390/genes17091146","DOIUrl":"10.3390/genes17091146","url":null,"abstract":"<p><strong>Background: </strong>Hereditary cancer predisposition syndromes show a high risk of cancer development with germline pathogenic variants. Organ-specific surveillance has been recommended according to the causative gene. However, even among carriers of the same germline variants, developing cancer types are not always uniform. Tumor-normal paired comprehensive genomic profiling (CGP) enables the simultaneous assessment of germline and somatic variants in same patient. Correlations between germline variants and cancer types have been reported; however, the significance of combinations of a germline variant and somatic variants remain unclear in the development of cancer types.</p><p><strong>Methods: </strong>In this study, we analyzed the correlation between pancreatic cancer and somatic variant patterns in patients with hereditary cancer predisposition syndrome, especially in patients with germline variants on <i>BRCA1</i>, <i>BRCA2</i>, or <i>ATM</i>.</p><p><strong>Results: </strong>Here, we show the characteristic pancreatic cancer patterns according to co-existing somatic variants in patients with germline pathogenic variants. The tumor-normal paired genetic data from 18,732 patients who underwent tumor-normal paired CGP were analyzed, including 853 germline-positive patients registered in a Japanese database. The combination of the somatic <i>TP53</i> variant and <i>KRAS</i> variant was closely correlated with the development of pancreatic cancer in patients with germline <i>BRCA1</i>, <i>BRCA2</i>, or <i>ATM</i>. In particular, the somatic <i>KRAS</i> variant was significantly associated with pancreatic cancer.</p><p><strong>Conclusions: </strong>These findings suggest that pancreatic cancer of hereditary cancer syndromes might be associated with co-existing somatic <i>KRAS</i> variants within the pancreas.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Genome Resequencing Reveals Genetic Diversity and Selective Sweep Signatures in Wuling Cattle.","authors":"Kunyou Xian, Yuee Gao, Zhiyi Su, Yating Wei, Kai Yang, Zexuan Hong, Xiaoqian Wu, Jicai Zhang, Halima Jafari, Chuzhao Lei, Ankui Wang","doi":"10.3390/genes17091141","DOIUrl":"10.3390/genes17091141","url":null,"abstract":"<p><p><b>Background</b>: Wuling cattle are a native breed in southern China and primarily inhabit mountainous regions. They are distributed across three geographically distinct mountainous regions and were historically classified into three local populations: Enshi cattle (western Hubei), Sinan cattle (eastern Guizhou) and Xiangxi cattle (western Hunan). Here, we aim to elucidate the genetic relationships and describe the genetic characteristics of Wuling cattle across these regions. <b>Methods</b>: We performed whole-genome resequencing of 20 Sinan cattle, together with public data of 10 Enshi cattle, 20 Xiangxi cattle and 65 cattle from four reference continental groups. Reads were aligned to the ARS-UCD1.2 reference genome. Genetic differences between different cattle breeds were assessed through analyses of population structure and genetic diversity. Selective signals in Wuling cattle were identified using single-population selective analysis and local ancestry inference, whilst potential differences between different Wuling cattle subpopulations were pinpointed using cross-population selective analysis. <b>Results</b>: On the basis of whole-genome resequencing data, Enshi, Sinan and Xiangxi cattle share highly similar genetic backgrounds (with similar ancestral lineages comprising East Asian taurine and East Asian indicine) and negligible genetic differentiation (the pairwise <i>F_ST</i> among Enshi cattle, Sinan cattle and Xiangxi cattle was approximately 0.01), supporting their classification as a single breed-Wuling cattle. Selective sweep analysis in Wuling cattle revealed multiple genomic regions under selection associated with key biological processes, including reproduction, fat deposition, feed efficiency, skeletal and muscle development, and immune response. Part of these regions is derived from East Asian indicine, related with <i>SYTL1</i>, <i>TMEM222</i>, <i>WDTC1</i> and <i>SLC9A1</i>. Furthermore, Wuling cattle are found in various regions, where geographical conditions vary. Distinct selective signals were also observed among regional groups of Wuling cattle, likely reflecting adaptation to their diverse local environments. <b>Conclusions</b>: This study provides a comprehensive genomic characterization of Wuling cattle, outlines the selection signals for Wuling cattle, whilst demonstrating that different geographical environments have generated unique selection pressures within the Wuling cattle population. Providing a genetic guidelines for the conservation and sustainable utilization of their genetic resources.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subgenome-Resolved Analysis and Regulatory Divergence of UDP-Glycosyltransferases in Allotetraploid <i>Panax ginseng</i>.","authors":"Qizhan Guo, Xin He, Lingping Yang, Xiaojuan Tian, Mingxu Wu, Ting Zhang, Liying Feng, Anqiang Jia","doi":"10.3390/genes17091140","DOIUrl":"10.3390/genes17091140","url":null,"abstract":"<p><p><b>Background</b>: Polyploidization generates extensive gene redundancy, but how duplicated metabolic genes are retained and subsequently diversified remains poorly understood. UDP-glycosyltransferases (UGTs) provide a suitable system for examining this process because they participate in specialized metabolism, plant development, and environmental responses. This study aimed to characterize the retention, expansion, and regulatory divergence of the UGT family in allotetraploid <i>Panax ginseng</i> at subgenome resolution. <b>Methods</b>: We integrated telomere-to-telomere (T2T) genome annotation, phylogenetic and chromosomal analyses, duplication classification, collinearity and <i>Ka</i>/<i>Ks</i> analyses, promoter cis-acting element prediction, developmental co-expression networks, and transcriptomic responses to biotic and abiotic treatments. <b>Results</b>: A total of 212 <i>PgUGT</i> genes were identified, including 104 and 108 members in the A and B subgenomes, respectively. The family exhibited an overall near-mirrored retention pattern between the two subgenomes, accompanied by local copy-number asymmetry. Whole-genome and segmental duplication accounted for 64.2% of the family, and 99.5% of the gene pairs with valid <i>Ka</i>/<i>Ks</i> estimates had values below 1, suggesting pervasive purifying selection. <i>PgUGT</i>-containing co-expression modules were associated with bud, stem, leaf, and fruit developmental conditions, while promoter cis-acting element compositions exhibited member-specific variation. Transcriptional responses to fungal pathogens and abiotic, hormone, and chemical treatments were concentrated in particular members and local gene arrays rather than being coordinated across entire clades or subgenomes. <b>Conclusions</b>: The <i>PgUGT</i> family is characterized by extensive ancestral copy retention accompanied by local copy-number changes and copy-specific regulatory divergence. These findings provide a subgenome-resolved framework for understanding UGT family evolution in allotetraploid ginseng and prioritize candidate <i>PgUGT</i> genes for subsequent functional validation.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Transcriptomics Reveals Divergent Expression Patterns Related to Carbon Metabolism, Transport, and Regulation in Juvenile Stems of Four Fagaceae Species.","authors":"Xiyuan Yang, Liwen Wu, Yangdong Wang","doi":"10.3390/genes17091139","DOIUrl":"10.3390/genes17091139","url":null,"abstract":"<p><p><b>Background/Objectives:</b> We compared juvenile whole-stem transcriptomes of <i>Quercus glauca</i>, <i>Quercus acutissima</i>, <i>Quercus fabri</i>, and <i>Castanopsis sclerophylla</i> to examine carbon metabolism and transport. <b>Methods:</b> Three seedlings per species were sampled in one session. RNA sequencing (RNA-seq) data were analyzed using differential-expression analysis, direction-specific Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, gene set enrichment analysis (GSEA), and leading-edge analysis. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed on aliquots from the same RNA extractions. <b>Results:</b> Reference-based analyses identified 8596-11,823 differentially expressed genes across six contrasts. GSEA detected 25 significant pathway-by-contrast associations across 13 pathways at a false discovery rate below 0.05. <i>Q. glauca</i> showed photosynthesis, starch turnover, and flavonoid pathway signals. <i>Q. acutissima</i> showed sugar-metabolism and ATP-binding cassette (ABC) transport signals, with <i>XTH23</i> providing an annotation-based wall-remodeling candidate. <i>Q. fabri</i> showed enrichment of sulfur amino acid metabolism, nucleotide sugar metabolism, and mitogen-activated protein kinase signaling. <i>C. sclerophylla</i> showed ABC transport and galactose metabolism enrichment, with candidates annotated for raffinose synthesis and extracellular sucrose cleavage. Eleven of 12 candidates were present in at least one significant GSEA leading edge; <i>XTH23</i> was selected using differential expression and annotation. Both assays identified the same species as having the highest expression for every candidate; eight genes also showed the same rank order across all four species. <b>Conclusions:</b> The sampled stems differed in the expression of genes associated with carbon metabolism, transport, and regulation. These whole-stem patterns provide candidates for tissue-resolved and physiological studies.</p>","PeriodicalId":12688,"journal":{"name":"Genes","volume":"17 9","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13606254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149060297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}