Genes & genomics最新文献

{"title":"Integrative bioinformatics approaches reveal key hub genes in cyanobacteria: insights from Synechocystis sp. PCC 6803 and Geminocystis sp. NIES-3708 under abiotic stress conditions.","authors":"Abbas Karimi-Fard, Abbas Saidi, Masoud Tohidfar, Seyede N Emami","doi":"10.1007/s13258-025-01615-0","DOIUrl":"10.1007/s13258-025-01615-0","url":null,"abstract":"<p><strong>Background: </strong>Cyanobacteria, particularly Synechocystis sp. PCC 6803, serve as model organisms for studying acclimation strategies that enable adaptation to various environmental stresses. Understanding the molecular mechanisms underlying these adaptations provides insight into how cells adjust gene expression in response to challenging conditions.</p><p><strong>Objective: </strong>To analyze the transcriptome data of Synechocystis sp. PCC 6803 under light, salinity, and iron stress conditions and to identify hub genes potentially involved in stress response, specifically comparing the findings with Geminocystis sp. NIES-3708.</p><p><strong>Methods: </strong>A comprehensive bioinformatics approach was applied, integrating meta-analysis, weighted gene co-expression network analysis (WGCNA), and a Random Forest (RF) machine learning algorithm. These approaches underscore the robustness of our findings, allowing for a more nuanced understanding of gene interactions and their functional relevance in stress responses. This methodology was used to identify key hub genes in Synechocystis sp. PCC 6803 that may have conserved roles in Geminocystis sp. NIES-3708. A total of four potential hub genes, including slr1392, slr1484, sll1549, and sll1863, were identified. Among these, only sll1549 had a homolog (GM3708_2556) with 71% sequence similarity and 70% query coverage in Geminocystis sp. NIES-3708. The expression of GM3708_2556 was further evaluated under nitrate, salt, and combined salinity-nitrate stress conditions using RT-qPCR.</p><p><strong>Results: </strong>Transcript levels of GM3708_2556 increased significantly under salt stress (3.35-fold, p-value < 0.05) and combined salinity-nitrate stress (2.24-fold, p-value < 0.05) compared to control conditions, while no significant change was observed under nitrate stress alone. These results suggest that GM3708_2556 may play a crucial role in the organism's response to salt stress, with potential interactions in nitrate metabolism.</p><p><strong>Conclusion: </strong>This study highlights the gene GM3708_2556 as a significant factor in salt stress response, with implications for conserved functional roles across cyanobacterial species. Furthermore, the findings have potential relevance to biotechnology, particularly in engineering stress-resistant cyanobacterial strains for applications in sustainable agriculture and bioenergy production.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"383-397"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028598","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":"Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.","authors":"Seula Keum, Yoon Ji Lee, Jung-Woong Kim, Sangmyung Rhee","doi":"10.1007/s13258-024-01604-9","DOIUrl":"10.1007/s13258-024-01604-9","url":null,"abstract":"<p><strong>Background: </strong>The mechanical remodeling of tumor microenvironment is critical for non-small cell lung cancer (NSCLC) progression. Dual-specificity phosphatase 23 (DUSP23) has been previously identified as a mechano-responsive gene, but its role in NSCLC progression remains unknown.</p><p><strong>Objective: </strong>We aim to elucidate the clinical significance of DUSP23 in NSCLC progression.</p><p><strong>Methods: </strong>We analyzed the expression of DUSP23 in cancer using polyacrylamide hydrogels designed to mimic the stiffness of normal (soft; ~0.5 kPa) and cancerous (stiff; ~40 kPa) tissues. The prognostic significance of DUSP23 expression in patients was examined using public databases. Additionally, we conducted various cell-based assays and transcriptomic analyses in DUSP23-silenced NSCLC cell lines. A risk score prognosis model was constructed using univariate Cox regression and Kaplan-Meier analysis.</p><p><strong>Results: </strong>Our findings show that DUSP23 is upregulated in stiff matrices and is highly associated with poor prognosis in patients with solid cancers such as NSCLC and breast cancer. Silencing of DUSP23 resulted in decreased cell proliferation and invasion. Transcriptomic profiling revealed that 182 genes were downregulated, and 230 genes upregulated following DUSP23-depletion. Notably, 182 downregulated genes were enriched in cancer-related pathways, including cell cycle progression and cytoskeleton organization. Through KEGG pathway analysis, we identified 11 cancer-related genes and developed a prognostic risk model. In this model, the high-risk group of NSCLC patients exhibited significantly shorter overall survival compared to low-risk group, based on public datasets.</p><p><strong>Conclusion: </strong>Our study demonstrates the clinical significance of DUSP23 as a prognostic marker in NSCLC and highlights its potential role of DUSP23 in promoting NSCLC progression.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"321-329"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846492","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 novel frameshift TBX4 variant in a family with ischio-coxo-podo-patellar syndrome and variable severity.","authors":"Giada Moresco, Ornella Rondinone, Alessia Mauri, Rita Gorgoglione, Daniela Maria Grazia Graziani, Michal Dziuback, Monica Rosa Miozzo, Silvia Maria Sirchia, Luca Pietrogrande, Angela Peron, Laura Fontana","doi":"10.1007/s13258-024-01589-5","DOIUrl":"10.1007/s13258-024-01589-5","url":null,"abstract":"<p><strong>Background: </strong>Congenital anomalies of the knee are a spectrum of rare disorders with wide clinical and genetic variability, which are mainly due to the complex processes underlying knee development. Despite progresses in understanding pathomechanisms and associated genes, many patients remain undiagnosed.</p><p><strong>Objective: </strong>To uncover the genetic bases of a congenital patellar dislocation affecting multiple family members with variable severity.</p><p><strong>Methods: </strong>We performed ES in the proband and his father, both showing bilateral patellar dislocation, his sister with a milder similar condition, and his unaffected mother. Sanger sequencing was then performed in the proband's brother and paternal aunt, both affected as well.</p><p><strong>Results: </strong>ES and Sanger sequencing identified the presence of the novel heterozygous frameshift mutation c.735delT in the TBX4 gene in all affected family members. TBX4 is associated with autosomal dominant ischio-coxo-podo-patellar syndrome with/without pulmonary arterial hypertension (ICPPS, #147891), reaching a diagnosis in the family. Intrafamilial clinical heterogeneity suggests that other factors might be involved, such as additional variants in TBX4 or in other modifier genes. Interestingly, we identified three additional variants in the TBX4 gene in the proband only, whose phenotype is more severe. Despite being classified as benign, one of these variants is predicted to disrupt a splicing protein binding site, and may therefore affect TBX4 alternative splicing, accounting for the more severe phenotype of the proband.</p><p><strong>Conclusion: </strong>We expand and further delineate the genotypic and phenotypic spectrum of ICPPS. Further studies are necessary to shed light on the potential effect of this variant and on the variable phenotypic expressivity of TBX4-related phenotypes.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"341-349"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521713","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 novel CDH23 heterozygous variants causing autosomal recessive nonsyndromic hearing loss.","authors":"Baoqiong Liao, Wuming Xie, Rutian Liu, Qi Zhang, Ting Xie, Dan Jia, Shuwen He, Hailong Huang","doi":"10.1007/s13258-024-01611-w","DOIUrl":"10.1007/s13258-024-01611-w","url":null,"abstract":"<p><strong>Background: </strong>Hearing loss adversely impacts language development, acquisition, and the social and cognitive maturation of affected children. The hearing loss etiology mainly includes genetic factors and environmental factors, of which the former account for about 50-60%.</p><p><strong>Objective: </strong>This study aimed to investigate the genetic basis of autosomal recessive non-syndromic hearing loss (NSHL) by identifying and characterizing novel variants in the CDH23 gene. Furthermore, it seeks to determine the pathogenic potential of the noncanonical splice site variant c.2398-6G > A.</p><p><strong>Methods: </strong>Comprehensive clinical evaluation and whole-exome sequencing (WES) were performed on the girl. The WES analysis revealed two novel variants in the CDH23 gene, associated with nonsyndromic deafness 12 (DFNB12). To further explore the pathogenicity of these variants, functional studies involving in vivo splicing analysis were performed on the novel noncanonical splice site variant, c.2398-6G > A, which was initially classified as a variant of uncertain significance (VUS).</p><p><strong>Results: </strong>Whole-exome sequencing of the patient identified two compound heterozygous variants in CDH23: c.2398-6G > A, a noncanonical splice site variant, and c.6068C > A (p. Ser2023Ter), a nonsense mutation. In vitro splicing assays demonstrated that c.2398-6G > A caused aberrant splicing, leading to a frameshift (p. Val800Alafs*6) and the production of a truncated protein, as confirmed by structural protein analysis. The study revealed novel mutations as likely pathogenic, linking both variants to autosomal recessive NSHL.</p><p><strong>Conclusions: </strong>Our analyses revealed novel compound heterozygous mutations in CDH23 associated with autosomal recessive NSHL, thereby expanding the mutational landscape of CDH23-related hearing loss and increasing knowledge about the CDH23 splice site variants.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"293-305"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947492","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":"CTHRC1 expresses in cancer-associated fibroblasts and is associated with resistance to anti-androgen therapy in prostate cancer.","authors":"Hai-Qi Liang, Qi-Huan He, Qiu-Ju Wei, Qi-Zhou Mo, Guang-Lin Yang, Fa-Ye Wei, Li-Wei Wei, Yu-Jian Li, Min Qin, Ji-Wen Cheng","doi":"10.1007/s13258-025-01624-z","DOIUrl":"https://doi.org/10.1007/s13258-025-01624-z","url":null,"abstract":"<p><strong>Background: </strong>CTHRC1 overexpresses in prostate cancer and is associated with the proliferation, invasion and migration of prostate cancer cells. However, the roles and mechanisms of CTHRC1 expression in prostate cancer prognosis and treatment outcomes remain unknown.</p><p><strong>Objective: </strong>This study aimed to explore the expression and gene function of CTHRC1 in prostate cancer, investigate the prognostic value and potential effect in the treatment of prostate cancer.</p><p><strong>Methods: </strong>Bulk and single-cell RNA sequencing analyses were used to evaluate the expression of CTHRC1 in prostate cancer. All data used in the study were obtained from publicly available sources to ensure transparency. Study enrolled 1999 cases of prostate cancer and 531 normal controls. Single-cell RNA sequencing profile included 62,995 cells from seven prostate primary tumors. CTHRC1 expression and prognosis analyses were conducted with these samples and verified by immunohistochemical staining. CIBERSORT algorithm was used to assess the tumor immune infiltrating cells based on bulk mRNA sequencing profiles. Genomics of drug sensitivity in cancer (GDSC) database was used to predict IC50 to anti-androgen therapy (ADT) drugs of the samples.</p><p><strong>Results: </strong>CTHRC1 expressed in prostate cancer was higher than that in normal prostate tissue, and the expression increased with the progress of prostate cancer. CTHRC1 was the risk factor of progression-free interval (PFI). CTHRC1 was positively correlated with the infiltration of tumor-associated macrophages (TAMs). Myofibroblast-like cancer-associated fibroblasts (myCAFs) were the major CTHRC1 expressers in prostate cancer. TGF-β signaling activated in CTHRC1-positive myCAFs and was involved in TAMs polarization. Biological functions of myCAFs were enriched in hormone response and metabolism. CTHRC1 may regulate androgen receptor signaling through CCN2/CAV1/AR pathway. Moreover, ADT drug Bicalutamide and AZD3514 were less sensitive in the high CTHRC1 expression tumors.</p><p><strong>Conclusions: </strong>As a potential molecular target of ADT resistance in prostate cancer, CTHRC1 provides a new promising molecular approach for the diagnosis and treatment of prostate cancer.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500585","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":"Integrative analysis of genetic variability and functional traits in lung adenocarcinoma epithelial cells via single-cell RNA sequencing, GWAS, bayesian deconvolution, and machine learning.","authors":"Chenggen Gao, Jintao Wu, Fangyan Zhong, Xianxin Yang, Hanwen Liu, Junming Lai, Jing Cai, Weimin Mao, Huijuan Xu","doi":"10.1007/s13258-025-01621-2","DOIUrl":"https://doi.org/10.1007/s13258-025-01621-2","url":null,"abstract":"<p><strong>Background: </strong>Lung adenocarcinoma remains a leading cause of cancer-related mortality worldwide, characterized by high genetic and cellular heterogeneity, especially within the tumor microenvironment.</p><p><strong>Objective: </strong>This study integrates single-cell RNA sequencing (scRNA-seq) with genome-wide association studies (GWAS) using Bayesian deconvolution and machine learning techniques to unravel the genetic and functional complexity of lung adenocarcinoma epithelial cells.</p><p><strong>Methods: </strong>We performed scRNA-seq and GWAS analysis to identify critical cell populations affected by genetic variations. Bayesian deconvolution and machine learning techniques were applied to investigate tumor progression, prognosis, and immune-epithelial cell interactions, particularly focusing on immune checkpoint markers such as PD-L1 and CTLA-4.</p><p><strong>Results: </strong>Our analysis highlights the importance of genes like SLC2A1, which regulates glucose metabolism and correlates with tumor invasiveness and poor prognosis. Immune-epithelial interactions suggest a suppressive tumor microenvironment, potentially hindering immune responses. Additionally, machine learning models identify core prognostic genes such as F12, GOLM1, and S100P, which are significantly associated with patient survival.</p><p><strong>Conclusions: </strong>This comprehensive approach provides novel insights into lung adenocarcinoma biology, emphasizing the role of genetic and immune factors in tumor progression. The findings support the development of personalized therapeutic strategies targeting both tumor cells and the immune microenvironment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482886","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 regulating the lung carcinoma progression via inhibiting ubiquitin-proteasomal degradation to increase MMP9 protein stability.","authors":"Jie Zhao, Juanjuan Dai, Ning Zhou, Dongqin Liu, Dandan Wang, Shuang Miao, Chao Liang, Di An, Jiatong Jiang, Kaikai Gong, Yan Wu","doi":"10.1007/s13258-025-01623-0","DOIUrl":"https://doi.org/10.1007/s13258-025-01623-0","url":null,"abstract":"<p><strong>Background: </strong>Non-small-cell-lung-cancer (NSCLC) is a prevalent lung malignancy among humans. UBE2C is a critical component of the ubiquitin-proteasome system, and its expression level is significantly associated with cancer development and cell proliferation. Nevertheless, the mechanisms of UBE2C in NSCLC remain unclear.</p><p><strong>Objective: </strong>We aimed to investigate the role of MMP9 in UBE2C-overexpressed NSCLC progression.</p><p><strong>Methods: </strong>The GEPIA database and Kaplan-Meier curves were used to determine UBE2C expression in human tumors and survival in NSCLC. CCK8, colony formation, and Transwell^® assays were employed to assess the function of UBE2C in vitro. Western blotting, immunofluorescence assay, and RT-qPCR were utilized to determine protein and mRNA expression levels. CHX chase and co-immunoprecipitation assays were used to elucidate the regulatory mechanism.</p><p><strong>Results: </strong>This research proved that UBE2C expression was related to patient overall survival, cell proliferation and migration. Furthermore, overexpressed UBE2C could promote the protein stability of Matrix metalloproteinase-9 (MMP9) to upregulate its protein level in NSCLC cells. Meanwhile, UBE2C upregulation promoted lung carcinoma progression by modulating MMP9 expression.</p><p><strong>Conclusions: </strong>Our findings indicate that UBE2C may be a therapeutic and prognostic target for lung carcinoma.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457591","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":"Potential role of ARG1 c.57G > A variant in Argininemia.","authors":"Yixiao Li, Rujin Tian, Dong Wang, Haozheng Zhang, Yi Zhou, Chunli Ma, Han Zhang, Kaihui Zhang, Shu Liu","doi":"10.1007/s13258-024-01595-7","DOIUrl":"10.1007/s13258-024-01595-7","url":null,"abstract":"<p><strong>Background and objective: </strong>Argininemia (OMIM: 207800), as well as arginase deficiency, a disorder of the urea cycle caused by deficiency of arginase 1 (ARG1, NP_000036.2), is a scarce autosomal recessive genetic disease. The patients who suffered with argininemia often showed spastic paraplegia, epileptic seizures, severe mental retardation, and even the hyperammonemia. In neonatal screening, we found a healthy baby with mild elevated arginine levels. We have demonstrated the genetic etiology of the patient.</p><p><strong>Methods: </strong>The patient's clinical characteristic and family history were collected. The technologies including Next Generation Sequencing (NGS), Sanger sequencing, Bioinformatics Analysis, RNA extraction, cDNA obtained, Sanger sequencing, Minigene splicing assay, Real-time PCR, Single-molecule real-time (SMRT) sequencing were applied.</p><p><strong>Results: </strong>One homozygous variant, c.57G > A (p.Q19=), was identified in the proband, which was inherited from the parents. Through different detection methods, we found that the c.57G > A variant causes three different transcriptional versions: normal mRNA (mRNA from blood), mRNA with the exon2 deletion (73bp, mRNA from blood and minigene assay), and mRNA sequence from the SMRT sequencing (parts of exons and introns were detected, including exon 1-4, intron 1 and 4, and part of intron 2, 3, and 5). The expression of ARG1 mRNA and protein also decreased in the blood. The related genes of NMD (Nonsense-mediated mRNA decay), SMG1, UPF1, and UPF3b, were expressed higher than the controls in the blood, which hints the NMD could play a role in the mRNA decay regarding the cDNA with 73bp deletion by c.57G > A variant.</p><p><strong>Conclusions: </strong>The study is the first study considering a synonymous variant of the ARG1 gene influencing alternative splicing(AS). Otherwise, the variant c.57G > A is relatively frequent in the general population( MAF = 0.0146). Our discovery revealed the variant possesses partial pathogenic potential, which would contribute to the deeper understanding and gold model for the intricate relationship between genetic mutations, arginine metabolism, and physical function.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"197-205"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681345","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":"Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle.","authors":"Dongmei Zhu, Xingmin Geng, Fanyu Zeng, Shida Xu, Jieyu Peng","doi":"10.1007/s13258-024-01593-9","DOIUrl":"10.1007/s13258-024-01593-9","url":null,"abstract":"<p><strong>Background: </strong>The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle).</p><p><strong>Objective: </strong>To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle.</p><p><strong>Methods: </strong>In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR).</p><p><strong>Results: </strong>We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds.</p><p><strong>Conclusion: </strong>In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"171-182"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681502","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 combination of upstream alleles involved in rice heading hastens natural long-day responses.","authors":"Myung-Shin Kim, Joung Sug Kim, Sang Ik Song, Kyong Mi Jun, Su-Hyeon Shim, Jong-Seong Jeon, Tae-Ho Lee, Sang-Bok Lee, Gang-Seob Lee, Yeon-Ki Kim","doi":"10.1007/s13258-024-01597-5","DOIUrl":"10.1007/s13258-024-01597-5","url":null,"abstract":"<p><strong>Background: </strong>The female parental line Jinbuol (JBO, early heading) and two recombinant isogenic lines, JSRIL1 and JSRIL2, have been shown to flower 44, 34 and 16 days earlier, respectively, than the male parental line Samgwang (SG, late heading) in paddy fields.</p><p><strong>Objective: </strong>To explore how photoperiodicity-related genes are involved in differential heading among these lines.</p><p><strong>Methods: </strong>Deep sequencing was conducted for these lines, photoperiodicity-related genes (71) were categorized, and qRT-PCR was performed for some key genes.</p><p><strong>Results: </strong>Deep sequencing revealed a nearly even contribution of parental groups, with 48.5% and 45% of the chromosomes in JSRIL1 and JSRIL2, respectively, inherited from the female parent JBO; however, Chr6 contained the most biased parental contribution, with 99.4% inherited from the female parent. The variation in single-nucleotide polymorphisms (SNPs) among many known flower-inducing genes, including rice GIGANTEA (OsGI); grain number, plant height and heading date 7 (Ghd7); and EARLY HEADING DATE 1 (Ehd1), was minimal. In the JSRILs, HEADING DATE 1 (Hd1) and VERNALIZATION INSENSITIVE 3-LIKE 1 (OsVIL2) originated from JBO, whereas FLAVIN-BINDING, KELCH REPEAT, F BOX 1 (OsFKF1) originated from SG. Interestingly, HEN1 suppressor 1 (OsHESO1) originated from SG in JSRIL1 and JBO in JSRIL2. RNA sequencing and qRT‒PCR analyses of plants at the floral meristem stage revealed that transcriptional regulation through chromosomal restructuring and posttranscriptional regulation might control minute gene regulation, resulting in delayed heading in JSRILs.</p><p><strong>Conclusion: </strong>Our gene expression and SNP analyses of elite recombinant isogenic lines could be helpful in understanding how photoperiodicity-related genes in rice are modulated.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"245-261"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11757646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681500","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}