Functional & Integrative Genomics最新文献

{"title":"Integrated multi-omics analysis and machine learning refine molecular subtypes and prognosis in hepatocellular carcinoma through O-linked glycosylation genes.","authors":"Minghao Li, Hongxu Li, Lei Liu, Qianyi Wei, Jie Gao, Bowen Hu, Zhihui Wang, Wenzhi Guo, Yi Zhang, Shuijun Zhang","doi":"10.1007/s10142-025-01669-z","DOIUrl":"10.1007/s10142-025-01669-z","url":null,"abstract":"<p><p>O-glycosylation significantly influences cellular physiological processes and disease regulation by modulating the structure, function, and stability of proteins. However, there is a notable gap in research focusing on O-glycosylation in relation to the prognosis of HCC patients. The study aimed to explore the expression and function of O-glycosylation genes in HCC from both bulk- and single-cell perspectives. Multi-omics data related to O-glycosylation identified by weighted gene co-expression network analysis (WGCNA). This was then combined with ten different clustering algorithms to construct molecular subtypes of high-resolution HCC. Cancer subtype 1 (CS1) is characterized by significant genomic variation, moderate immune cell infiltration, and immune function enrichment. Patients with CS2 have a better prognosis and are characterized by a stable genomic structure, an immune-hot phenotype with rich immune cell infiltration, and sensitivity to immunotherapy. CS3 is characterized by poor prognosis, outstanding genomic instability, and an immune-cold phenotype, but can benefit more from treatment with drugs such as sorafenib, cisplatin, paclitaxel, and gemcitabine. To further emphasize the role of O-glycosylation genes in individual HCC patients, we employed 59 machine-learning methods to construct and assess prognostic traits with improved generalizability. Microarray results indicated a pronounced upregulation of glycosylation hub genes involved in HCC stratification and modeling within HCC tumorous tissues. Altogether, our study highlights the importance of O-glycosylation for the assessment of HCC prognosis and treatment options by redefining HCC subtypes and constructing a consensus machine learning-driven prognostic signature (CMLS). This research establishes an optimized decision-making platform that enables the precise stratification of HCC patients, refines tumor treatment plans, and predicts patient survivability, with broad clinical implications.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"162"},"PeriodicalIF":3.1,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726375","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":"Analysis of the AP2/ERF transcription factor family in Eriobotrya japonica and its role in exogenous melatonin-mediated regulation of salt stress.","authors":"Ling Zhu, Fuhua Liu, Xin Lin, Tianyu Fu, Lin Zou, Yuanhai Pan, Rong Zou, Yang Zhao, Hanyao Zhang","doi":"10.1007/s10142-025-01667-1","DOIUrl":"10.1007/s10142-025-01667-1","url":null,"abstract":"<p><p>AP2/ERF transcription factors (TFs) are involved in various regulatory pathways related to plant growth, development, and stress responses. The growth of Eriobotrya japonica, a popular fruit and medicinal plant, is affected by salt stress. Currently, the functions of E. japonica AP2/ERF in response to salt stress and its role in alleviating salt stress caused by exogenous melatonin (MT) remain unclear. Therefore, in this study, a bioinformatics approach was used to analyze the AP2/ERF TF family of E. japonica and its expression patterns under exogenous MT-regulated salt stress. A total of 187 AP2/ERF TFs on 18 chromosomes were identified in E. japonica, and phylogenetic analyses classified them into four subfamilies: AP2, ERF, DREB, and RAV. Each subfamily contains a relatively large number of biotic or abiotic stresses and hormone related cis-acting elements. There are 61 DEGs of EjAP2/ERF involved in the regulation of NaCl stress by exogenous melatonin. Among these genes,, seven DEGs were involved in the response to ethylene and defense signals under salt stress. These genes are involved in the regulation of NaCl-stressed E. japonica by exogenous MT by activating or repressing the transcription of downstream target genes. Notably, EjERF11, EjERF73, and EjERF86 may have functions similar to those of their homologous genes and may serve as vital genes for salt tolerance. This study is the first to investigate the functions of EjAP2/ERF genes in exogenous MT-regulated salt stress, and provides a theoretical foundation for exploring more features of AP2/ERF genes and a basis for breeding E. japonica with salt stress resistance.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"161"},"PeriodicalIF":3.1,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717232","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":"UBE2C: a potential therapeutic target and prognostic biomarker for prostate cancer patients.","authors":"Shan Li, Yang Liu, Xun Wu, Qiuning Zhang, Wenzhen Yuan","doi":"10.1007/s10142-025-01671-5","DOIUrl":"https://doi.org/10.1007/s10142-025-01671-5","url":null,"abstract":"<p><p>UBE2C (Ubiquitin-conjugating enzyme E2C) has been confirmed to be closely associated with the progression of various cancers, but its specific role and clinical diagnostic and prognostic value in prostate cancer (PRAD) remain unclear. This study systematically assessed the expression characteristics, prognostic significance, and genetic mutations of UBE2C in cancer patients by integrating data from databases such as TCGA, GEO, cBioPortal, and COSMIC. Experimentally, we explored the biological functions of UBE2C in the occurrence and development of PRAD using various methods, including functional enrichment analysis, CCK8 cell proliferation assay, colony formation assay, Transwell migration and invasion assay, Edu staining, 3D tumor spheroid culture, cell cycle analysis, apoptosis detection, and xenograft tumor models. After knocking down UBE2C expression, the proliferation ability, migration and invasion ability of PRAD cells, as well as the growth of xenograft tumors, were all inhibited, and the cell cycle process and apoptosis were changed accordingly. These findings provide favorable experimental evidence and theoretical support for UBE2C as a novel molecular marker for prognosis assessment in solid tumors.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"159"},"PeriodicalIF":3.9,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706015","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":"ALKBH5-mediated NPC2 mRNA m⁶A demethylation promotes resistance to oxaliplatin in colorectal cancer.","authors":"Peng Wan, Yuan Ren, Hong-Tao Li","doi":"10.1007/s10142-025-01651-9","DOIUrl":"10.1007/s10142-025-01651-9","url":null,"abstract":"<p><p>Colorectal cancer (CRC) is the third most common cancer globally and a leading cause of cancer-related death. Oxaliplatin, a key platinum-based chemotherapy, significantly improves outcomes in CRC patients. Nevertheless, oxaliplatin resistance often emerges, leading to worse prognosis. Exploring new biomarkers and mechanisms of resistance is crucial for overcoming oxaliplatin resistance and enhancing therapeutic efficacy. Through bioinformatics analysis, high NPC2 expression was found to be associated with oxaliplatin resistance and poor prognosis in CRC patients. Moreover, NPC2 was highly expressed in CRC tissues, especially in metastatic CRC tissues. Additionally, the expression of N6-methyladenosine (m⁶A) demethylase ALKBH5 was elevated in oxaliplatin-resistant colorectal cancer cells. Mechanically, ALKBH5 promotes m⁶A demethylation of NPC2 mRNA in a YTHDF2-dependent process, thereby enhancing the stability of NPC2 mRNA and making colorectal cancer cells oxaliplatin-resistant. Our results show that by inhibiting NPC2 or ALKBH5, we can re-sensitize resistant CRC cells to oxaliplatin in vitro and in vivo. In summary, ALKBH5-mediated m⁶A demethylation promotes the stability of NPC2 mRNA and plays a key role in promoting oxaliplatin resistance in colorectal cancer. Targeting the ALKBH5/NPC2 axis have important therapeutic potential for patients with oxaliplatin-resistant colorectal cancer.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"158"},"PeriodicalIF":3.9,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144666805","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":"Integrating multiomics and modern breeding tools for accelerating genetic improvement in Annonas.","authors":"Shri Hari Prasad, Grant Bignell, Rhys G R Copeland, Vanika Garg, Annapurna Chitikineni, Robert J Henry, Natalie Dillon, Reyazul Rouf Mir, Rajeev K Varshney","doi":"10.1007/s10142-025-01653-7","DOIUrl":"10.1007/s10142-025-01653-7","url":null,"abstract":"<p><p>Custard apples (Annona spp.) are among the most important horticultural crops in the world, including Australia. The genus Annona comprises several economically and nutritionally significant species, including atemoya, cherimoya, sugar apple, ilama, soursop, bullock's heart, and bibra. These fruits are valued for their exotic taste and are popular backyard fruit crops in many countries. While some species are commercially cultivated and exported, the broader potential of these crops remains largely untapped. Despite their historical significance, these Annona species remain neglected or underutilised, with breeding efforts restricted to only a few countries. Extensive genetic resources, including germplasm collections, candidate genotypes, and mapping populations, are available for crop improvement. Traditional breeding methods - such as selection, crossbreeding, and mutation breeding - have been widely applied alongside modern breeding approaches like marker-assisted selection (MAS). However, several challenges, such as a lack of information regarding the crop and a long juvenile period, hinder crop improvement in custard apples. Recent advancements and affordability of sequencing technologies have enabled an increase in the number of multiomics studies, especially genomics and transcriptomics within Annona species. Integrating these data with proteomics, metabolomics, and phenomics will facilitate the genetic dissection of important traits in Annona. This review provides a comprehensive overview of the current advancements and future prospects of multiomics tools and technologies developed and their potential to accelerate custard apple breeding programs.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"155"},"PeriodicalIF":3.9,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615675","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":"Methyltransferase ZC3H13 regulates ferroptosis of alveolar macrophages in sepsis-associated acute lung injury via PRDX6/p53/SLC7A11 axis.","authors":"Jifang Liang, Zemin Liu, Yajun He, Heihei Li, Weidong Wu","doi":"10.1007/s10142-025-01659-1","DOIUrl":"https://doi.org/10.1007/s10142-025-01659-1","url":null,"abstract":"<p><p>Peroxiredoxin 6 (PRDX6) is widely acknowledged as a suppressor of ferroptosis, and recent studies have demonstrated that inhibition of macrophage ferroptosis can alleviate sepsis-associated acute lung injury (SA-ALI). Nonetheless, the specific involvement of PRDX6 in regulating macrophage ferroptosis during SA-ALI remains unexplored. This study aims to elucidate the mechanistic role of PRDX6 in modulating macrophage ferroptosis within the context of SA-ALI. Mouse alveolar macrophages (MH-S cells) were infected with either a PRDX6 overexpression lentivirus or a ZC3H13 knockdown lentivirus prior to lipopolysaccharide (LPS) treatment. In vivo, mice were treated with the same lentiviral constructs and subjected to a SA-ALI model via cecal ligation and puncture (CLP). This study demonstrates that PRDX6 overexpression or ZC3H13 knockdown significantly attenuated LPS-induced ferroptosis in alveolar macrophages and alleviated lung injury in CLP-induced SA-ALI mouse models. However, simultaneous knockdown of both ZC3H13 and PRDX6 abolished the protective effect conferred by ZC3H13 silencing, indicating that PRDX6 mediates the anti-ferroptotic role of ZC3H13 inhibition. Mechanistically, PRDX6 suppresses p53 expression, thereby upregulating SLC7A11 and inhibiting ferroptosis. Additionally, ZC3H13 promotes the m6A modification of PRDX6 mRNA, which facilitates its degradation in a YTHDF2-dependent manner, ultimately leading to reduced PRDX6 expression. Overall, these findings demonstrate that the methyltransferase ZC3H13 modulates PRDX6 expression by elevating the m6A methylation level of PRDX6 mRNA in a YTHDF2-dependent manner, thereby influencing the p53/SLC7A11 axis and promoting ferroptosis in alveolar macrophages, ultimately contributing to the progression of SA-ALI.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"156"},"PeriodicalIF":3.9,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144615676","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":"Integration of scRNA-seq and bulk tissue RNA-seq data to identify cancer-associated fibroblast-related gene RGMA as a potential treatment target for esophageal cancer.","authors":"Yanqing Gao, Shuguang Bao, Bao Wen, Haoyuan Li, Qiang Guo, Ao Li, Luri Bao, Meitao Li, Bateer Han","doi":"10.1007/s10142-025-01660-8","DOIUrl":"10.1007/s10142-025-01660-8","url":null,"abstract":"<p><p>Cancer-associated fibroblasts (CAFs) serve as key stromal components within tumor microenvironment (TME), playing a significant role in the development and outcome of esophageal cancer (EC). There is an urgent need to identify genes related to CAFs to improve treatment strategies. The scRNA-sequencing dataset GSE196756 were used to identify fibroblast-related genes. Additionally, a WGCNA analysis was also conducted to identify modules related to CAFs within the TCGA-esophageal carcinoma (ESCA) cohort. By taking the intersection of identified genes of these two sections, CAF-related genes were identified. Expression of RGMA in EC samples compared to normal controls was assessed by RT-qPCR and western blot. In vitro and in vivo experiments were conducted to assess the impact of RGMA on EC cell growth. Compared to adjacent normal tissues, the levels of RGMA were notably reduced in EC tissues. Reduced RGMA levels were linked to a poor prognosis for EC patients. Furthermore, RGMA was found to have a positive correlation with the expression of fibroblast-related gene DCN, and showed a negative correlation with the expression of tumor-promoting chemokines, CXCL1, CXCL3 and CXCL8. Functionally, RGMA overexpression strongly prevented ECA109 cell viability, proliferation and migration, as well as suppresses tumor growth in vivo, suggesting that RGMA may function as a tumor suppressor in EC. Additionally, RGMA levels were also remarkably decreased in human esophageal CAFs relative to esophageal fibroblast cells (NFs). Importantly, the downregulation of RGMA may facilitate the transdifferentiation of NFs into CAFs by activating Akt signaling or upregulating CXCL1, CXCL3, and CXCL8, subsequently contributing to ECA109 cell proliferation. Collectively, RGMA may serve as a prognostic marker and a potential therapeutic target for EC. Clinical trial number Not applicable.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"154"},"PeriodicalIF":3.1,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607005","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":"SPP1 promotes malignant characteristics and drug resistance in hepatocellular carcinoma by activating fatty acid metabolic pathway.","authors":"Zhijiang Wang, Chengfang Wang","doi":"10.1007/s10142-025-01664-4","DOIUrl":"https://doi.org/10.1007/s10142-025-01664-4","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) progression and prognosis are influenced by various molecular markers. This study aimed to identify the hub gene associated with HCC clinical characteristics and its role in HCC progression. Differentially expressed genes (DEGs) between HCC tumor and normal tissues, as well as between stage I/II and stage III/IV, were analyzed. Machine learning algorithms were used to pinpoint three critical hub genes (SPP1, ADH4, and ANXA10). A prognostic risk model was constructed and evaluated using Kaplan-Meier curves, COX regression, and decision curve analysis, which could effectively predict HCC survival. Among the three hub genes, SPP1 was significantly associated with the overall survival (OS) of HCC patients and effectively predicted prognosis. More importantly, SPP1 was upregulated in HCC tumor tissues and cells, and its overexpression enhanced HCC cell proliferation, migration, invasion, and drug resistance. It also promoted fatty acid metabolism in HCC cells, with malignant characteristics and drug resistance induced by SPP1 being mitigated by fatty acid oxidation inhibition. In vivo experiments showed that SPP1 knockdown inhibited tumor growth and fatty acid metabolism of HCC mice. In conclusion, SPP1 is a pivotal gene that influences HCC prognosis by enhancing malignancy and drug resistance through fatty acid metabolism.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"151"},"PeriodicalIF":3.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607006","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":"USP6NL knockdown suppresses colorectal cancer progression by inducing CASP9-Mediated apoptosis and disrupting FOXC2/SNAI1-Driven EMT and angiogenesis.","authors":"Mohammed Ahmed Mohammed, Ahmed Abdelmagied Soffar, Amany I Yousef, Mohammed Salama, Fawziya A R Ibrahim, Tarek El-Sewedy, Alaa Elmetwalli","doi":"10.1007/s10142-025-01663-5","DOIUrl":"https://doi.org/10.1007/s10142-025-01663-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with tumor progression often driven by dysregulated oncogenic pathways. USP6NL, a known regulator of endocytic trafficking, has recently been implicated in tumorigenesis. However, its precise role in CRC remains unclear, and more studies are still needed to deepen our understanding of underlying mechanisms implicated in its oncogenic role. Therefore, silencing USP6NL could provide a novel therapeutic strategy by concurrently disrupting several oncogenic mechanisms, creating a new avenue for CRC management, particularly in patients who develop resistance against conventional therapies. This study investigates the impact of USP6NL knockdown on CRC cell morphology, proliferation, apoptosis, migration, angiogenesis, and metabolic adaptation, providing mechanistic insights into its oncogenic functions.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;HCT116 colorectal cancer cells were transfected with USP6NL-specific siRNA. Immunocytochemistry was used to confirm successful silencing, functional assays were performed to assess changes in cell morphology using phase-contrast and scanning electron microscopy, and colony formation and wound healing assays were performed to assess cell clonogenic capacity and migration, respectively, in addition to apoptosis assay via flow cytometry, and RT²-Profiler PCR array to measure variation in gene expression of 84 cancer-related genes. Statistical analyses were performed to evaluate significant differences between control and USP6NL-silenced groups.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;USP6NL depletion led to profound morphological changes, including membrane blebbing, cell shrinkage, and loss of adhesion, reflecting late apoptotic features of cells. These findings were further supported by flow cytometry, which confirmed increased apoptosis, with a higher proportion of late apoptotic cells (20.99% in USP6NL knockdown vs. 2.69% in control, p = 0.042). Colony formation assays revealed a significant reduction in the clonogenic potential, suggesting a critical role of USP6NL in promoting CRC cell proliferation (p ≤ 0.05). The wound healing assay demonstrated impaired migration in USP6NL-silenced cells, with a marked delay in wound closure (p = 0.0201 at 48 h). Gene expression analysis revealed a significant downregulation of VEGFC (-8.62-fold) and ANGPT2 (-4.03-fold), impairing angiogenesis and suppressing FOXC2, SNAI1, and SNAI2, indicating EMT inhibition. Additionally, CASP9, APAF1, and BCL2L11 were upregulated, confirming the activation of intrinsic apoptosis, while metabolic regulators HIF1A and LDHA were downregulated, suggesting impaired tumor hypoxic adaptation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study establishes USP6NL as a key modulator of CRC progression, regulating proliferation, apoptosis, migration, angiogenesis, and metabolic pathways. The loss of USP6NL leads to EMT suppression, apoptosis induction, ","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"153"},"PeriodicalIF":3.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607007","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":"Genome-wide characterization of invertases in Arabica coffee and its progenitors reveals putative genes involved in fruit development.","authors":"Gabriela Ester Ferraz, Robert Márquez Gutiérrez, Tiago Yukio Inoue, Gabriel de Campos Rume, Thais Aparecida Sales, Teodorico Castro Ramalho, Evandro Novaes, Dapeng Zhang, Antonio Chalfun-Junior, Flavia Maria Avelar Gonçalves","doi":"10.1007/s10142-025-01662-6","DOIUrl":"https://doi.org/10.1007/s10142-025-01662-6","url":null,"abstract":"<p><p>In plant physiological processes, invertases act by irreversibly degrading sucrose into hexoses, which actively contribute to plant growth and development. Few invertase genes have been characterized in Coffea, and consequently, the role of these enzymes in coffee plant development is not well understood. The present study conducted a genome-wide characterization of invertases in Arabica coffee and its diploid progenitors. A total of 65 invertase genes were identified, with 28 in C. arabica (CaINV), 18 in C. canephora (CcINV), and 19 in C. eugenioides (CeINV), with polyploidization being the primary cause of the expansion of the CaINV gene family. Synteny analyses and chromosomal mapping showed that the CaINV genes are mainly derived from C. eugenioides. The cis-acting elements suggested the involvement of invertase genes in three main categories: growth and development, responses to biotic and abiotic stress, and hormonal response. Transcriptome analyses showed that, except for the neutral/alkaline invertase gene CaN/AINV1, all invertase genes of C. arabica and C. canephora were expressed at different stages of fruit development, some constitutively and others conditionally. Although CaN/AINV1 was not expressed in the evaluated tissues, the presence of two GCN4 cis-elements suggests its involvement in specific processes in tissues or stages not analyzed in this study. Our results open many avenues for future studies in Coffea, especially for C. arabica and C. canephora, which are economically most significant and exhibit particularities regarding disease resistance, tolerance to abiotic stresses, and fruit chemical composition.</p>","PeriodicalId":574,"journal":{"name":"Functional & Integrative Genomics","volume":"25 1","pages":"152"},"PeriodicalIF":3.9,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607004","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}