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RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data. RiboParser/RiboShiny:用于全面分析和可视化核糖序列数据的集成平台。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-21 DOI: 10.1016/j.jgg.2025.04.010
Shuchao Ren, Yinan Li, Zhipeng Zhou
{"title":"RiboParser/RiboShiny: an integrated platform for comprehensive analysis and visualization of Ribo-seq data.","authors":"Shuchao Ren, Yinan Li, Zhipeng Zhou","doi":"10.1016/j.jgg.2025.04.010","DOIUrl":"10.1016/j.jgg.2025.04.010","url":null,"abstract":"<p><p>Translation is a crucial step in gene expression. Over the past decade, the development and application of Ribosome profiling (Ribo-seq) have significantly advanced our understanding of translational regulation in vivo. However, the analysis and visualization of Ribo-seq data remain challenging. Despite the availability of various analytical pipelines, improvements in comprehensiveness, accuracy, and user-friendliness are still necessary. In this study, we develop RiboParser/RiboShiny, a robust framework for analyzing and visualizing Ribo-seq data. Building on published methods, we optimize ribosome structure-based and start/stop-based models to improve the accuracy and stability of P-site detection, even in species with a high proportion of leaderless transcripts. Leveraging these improvements, RiboParser offers comprehensive analyses, including quality control, gene-level analysis, codon-level analysis, and the analysis of Ribo-seq variants. Meanwhile, RiboShiny provides a user-friendly and adaptable platform for data visualization, facilitating deeper insights into the translational landscape. Furthermore, the integration of standardized genome annotation renders our platform universally applicable to various organisms with sequenced genomes. This framework has the potential to significantly improve the precision and efficiency of Ribo-seq data interpretation, thereby deepening our understanding of translational regulation.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biallelic MED16 variants disrupt neural development and lead to an intellectual disability syndrome. 双等位基因MED16变异破坏神经发育并导致智力残疾综合征。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.004
Yan Huang, Zhenglong Xiang, Yaqin Xiang, Hu Pan, Mei He, Zhenming Guo, Oguz Kanca, Chen Liu, Zhao Zhang, Huaizhe Zhan, Yuan Wang, Qing-Ran Bai, Hugo J Bellen, Hua Wang, Shan Bian, Xiao Mao
{"title":"Biallelic MED16 variants disrupt neural development and lead to an intellectual disability syndrome.","authors":"Yan Huang, Zhenglong Xiang, Yaqin Xiang, Hu Pan, Mei He, Zhenming Guo, Oguz Kanca, Chen Liu, Zhao Zhang, Huaizhe Zhan, Yuan Wang, Qing-Ran Bai, Hugo J Bellen, Hua Wang, Shan Bian, Xiao Mao","doi":"10.1016/j.jgg.2025.04.004","DOIUrl":"10.1016/j.jgg.2025.04.004","url":null,"abstract":"<p><p>Mediator Complex Subunit 16 (MED16, MIM: 604062) is a member of the Mediator complex, which controls many aspects of transcriptional activity in all eukaryotes. Here, we report two individuals from a non-consanguineous family with biallelic variants in MED16 identified by exome sequencing. The affected individuals present with global developmental delay, intellectual disability, and dysmorphisms. To assess the pathogenicity of the variants, functional studies are performed in Drosophila and patient-derived cells. The fly ortholog med16 is expressed in neurons and some glia of the developing central nervous system (CNS). Loss of med16 leads to a reduction in eclosion and lifespan, as well as impaired synaptic transmission. In neurons differentiated from the patient-derived induced pluripotent stem cells (iPSCs), the neurite outgrowth is impaired and rescued by expression of exogenous MED16. The patient-associated variants behave as loss-of-function (LoF) alleles in flies and iPSCs. Additionally, the transcription of genes related to neuronal maturation and function is preferentially altered in patient cells relative to differentiated H9 controls. In summary, our findings support that MED16 is important for appropriate development and function, and that biallelic MED16 variants cause a neurodevelopmental disease.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Harnessing lysosomal genetics: development of a risk stratification panel and unveiling of DPP7 as a biomarker for colon adenocarcinoma. 利用溶酶体遗传学:风险分层面板的发展和DPP7作为结肠腺癌的生物标志物的揭示。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.009
Zhengdong Luo, Yanlei Wang, Shunjie Zeng, Longchen Yu, Yuxiao Zhao, Hong Wang, Yingjing Fan, Yanli Zhang, Lili Wang, Yaping Li, Zhongfang Niu, Xin Zhang, Yi Zhang
{"title":"Harnessing lysosomal genetics: development of a risk stratification panel and unveiling of DPP7 as a biomarker for colon adenocarcinoma.","authors":"Zhengdong Luo, Yanlei Wang, Shunjie Zeng, Longchen Yu, Yuxiao Zhao, Hong Wang, Yingjing Fan, Yanli Zhang, Lili Wang, Yaping Li, Zhongfang Niu, Xin Zhang, Yi Zhang","doi":"10.1016/j.jgg.2025.04.009","DOIUrl":"10.1016/j.jgg.2025.04.009","url":null,"abstract":"<p><p>Lysosomal dysfunction has been implicated in the progression of colon adenocarcinoma (COAD), yet the prognostic significance and therapeutic potential of lysosome-related genes (LRGs) remain underexplored. In this study, we construct a 6-LRG-based prognostic risk stratification model (DPP7, ADAM8, CD1B, LRP2, ATP6V1C2, and PLAAT3) by integrating LASSO and Cox regression analyses. Stratifying patients based on median risk scores, we demonstrate that high-risk patients exhibit significantly worse clinical outcomes across the TCGA cohort and five independent GEO datasets. Furthermore, this panel outperforms 136 previously published models in terms of predictive accuracy for 1-, 3-, and 5-year survival rates. Validation multiplex immunofluorescence using an in-house tissue microarray cohort confirms the 6-LRG signature serves as an independent prognostic factor. Additionally, high-risk patients exhibit distinct immunosuppressive tumor microenvironment and aggressive malignancy characteristics. Functional depletion of DPP7 significantly inhibits tumor cell proliferation, migration, and metastasis in both in vitro and in vivo settings. Moreover, DPP7 silencing attenuates epithelial-mesenchymal transition, as evidenced by the upregulation of E-cadherin and downregulation of N-cadherin, Vimentin, and Snail. In conclusion, this study establishes an LRG-based model for COAD prognostic prediction and nominates DPP7 as a promising therapeutic target for COAD treatment.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Regulation of maize kernel development via divergent activation of α-Zein genes by transcription factors O11, O2, and PBF1. 转录因子O11、O2和PBF1通过α-玉米蛋白基因的发散激活调控玉米籽粒发育
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.008
Runmiao Tian, Zeyuan Yang, Ruihua Yang, Sihao Wang, Qingwen Shen, Guifeng Wang, Hongqiu Wang, Qingqian Zhou, Jihua Tang, Zhiyuan Fu
{"title":"Regulation of maize kernel development via divergent activation of α-Zein genes by transcription factors O11, O2, and PBF1.","authors":"Runmiao Tian, Zeyuan Yang, Ruihua Yang, Sihao Wang, Qingwen Shen, Guifeng Wang, Hongqiu Wang, Qingqian Zhou, Jihua Tang, Zhiyuan Fu","doi":"10.1016/j.jgg.2025.04.008","DOIUrl":"10.1016/j.jgg.2025.04.008","url":null,"abstract":"<p><p>α-Zeins, the major maize endosperm storage proteins, are transcriptionally regulated by Opaque2 (O2) and PROLAMIN-BOX BINDING FACTOR1 (PBF1), with Opaque11 (O11) functioning upstream of them. However, whether O11 directly binds to α-zein genes and its regulatory interactions with O2 and PBF1 remain unclear. Using the small-kernel mutant sw1, which exhibits decreased 19-kDa and increased 22-kDa α-zein, we positionally cloned O11 and found it directly binds to G-box/E-box motifs. O11 activates 19-kDa α-zein transcription, stronger than PBF1 but weaker than O2. Notably, PBF1 competitively binds to an overlapping E-box/P-box motif, and represses O11-mediated transactivation. Although O11 does not physically interact with O2, it participates in the O2-centered hierarchical network to enhance α-zein expression. sw1 o2 and sw1 pbf1 double mutants exhibit smaller, more opaque kernels with further reduced 19-kDa and 22-kDa α-zeins compared to the single mutants, suggesting distinct regulatory effects of these transcription factors on 19-kDa and 22-kDa α-zein genes. Promoter motif analysis suggests that O11, PBF1, and O2 directly regulate 19-kDa α-zein genes, while O11 indirectly controls 22-kDa α-zein genes via O2 and PBF1 modulation. These findings identify the unique and coordinated roles of O11, O2, and PBF1 in regulating α-zein genes and kernel development.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mammary stem cells: molecular cues, orchestrated regulatory mechanisms and its implications in breast cancer. 乳腺干细胞:分子线索,精心安排的调节机制及其在乳腺癌中的意义。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.007
Mengna Zhang, Lingxian Zhang, Jie Liu, Jiahui Zhao, Jiayu Mei, Jiahua Zou, Yaogan Luo, Cheguo Cai
{"title":"Mammary stem cells: molecular cues, orchestrated regulatory mechanisms and its implications in breast cancer.","authors":"Mengna Zhang, Lingxian Zhang, Jie Liu, Jiahui Zhao, Jiayu Mei, Jiahua Zou, Yaogan Luo, Cheguo Cai","doi":"10.1016/j.jgg.2025.04.007","DOIUrl":"10.1016/j.jgg.2025.04.007","url":null,"abstract":"<p><p>Mammary stem cells (MaSCs), endowed with self-renewal and multilineage differentiation capabilities, are crucial for mammary gland development, function, and disease initiation. Recent advances in MaSCs biology research encompass molecular marker identification, regulatory pathway dissection, and microenvironmental crosstalk. This review synthesizes key progress and remaining challenges in MaSC research. Molecular profiling advances have identified key markers recently, such as Procr, Dll1, Bcl11b, and PD-L1. Central to their regulatory logic are evolutionarily conserved pathways, including Wnt, Notch, Hedgehog, and Hippo, which exhibit context-dependent thresholds to balance self-renewal and differentiation. Beyond intrinsic signaling, the dynamic interplay between MaSCs and their microenvironment, such as luminal-derived Wnt4, macrophage-mediated TNF-α signaling, and adrenergic inputs from sympathetic nerves, spatially orchestrates stem cell behavior. In addition, this review also discusses the roles of breast cancer stem cells (BCSCs) in tumorigenesis and therapeutic resistance, focusing on the molecular mechanisms underlying MaSC transformation into BCSCs. Despite progress, challenges remain: human MaSCs functional assays lack standardization, pathway inhibitors risk off-target effects, and delivery systems lack precision. Emerging tools like spatial multi-omics, organoids, and biomimetic scaffolds address these gaps. By integrating MaSCs and BCSCs biology, this review links mechanisms to breast cancer and outlines strategies to target malignancy to accelerate clinical translation.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rhpn2 regulates the development and function of vestibular sensory hair cells through the RhoA signaling in zebrafish. Rhpn2通过RhoA信号通路调控斑马鱼前庭感觉毛细胞的发育和功能。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.006
Yubei Dai, Qianqian Li, Jiaju Deng, Sihang Wu, Guiyi Zhang, Yuebo Hu, Yuqian Shen, Dong Liu, Han Wu, Jie Gong
{"title":"Rhpn2 regulates the development and function of vestibular sensory hair cells through the RhoA signaling in zebrafish.","authors":"Yubei Dai, Qianqian Li, Jiaju Deng, Sihang Wu, Guiyi Zhang, Yuebo Hu, Yuqian Shen, Dong Liu, Han Wu, Jie Gong","doi":"10.1016/j.jgg.2025.04.006","DOIUrl":"10.1016/j.jgg.2025.04.006","url":null,"abstract":"<p><p>Hearing and balance disorders are significant health issues primarily caused by developmental defects or the irreversible loss of sensory hair cells (HCs). Identifying the underlying genes involved in the morphogenesis and development of HCs is crucial. Our current study highlights rhpn2, a member of rho-binding proteins, as essential for vestibular HC development. The rhpn2 gene is highly expressed in the crista and macula HCs. Loss of rhpn2 function in zebrafish reduces the otic vesicle area and vestibular HC number, accompanied by vestibular dysfunction. Shorter stereocilia and compromised mechanotransduction channel function are found in the crista HCs of rhpn2 mutants. Transcriptome RNA sequencing analysis predicts the potential interaction of rhpn2 with rhoab. Furthermore, co-immunoprecipitation confirms that Rhpn2 directly binds to RhoA, validating the interaction of the two proteins. rhpn2 knockout leads to a decreased expression of rock2b, a canonical RhoA signaling pathway gene. Treatment with the RhoA activator or exogenous rock2b mRNA injection mitigates crista HC stereocilia defects in rhpn2 mutants. This study uncovers the role of rhpn2 in vestibular HC development and stereocilia formation via mediating the RhoA signaling pathway, providing a target for the treatment of balance disorders.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
GCH1 contributes to high-altitude adaptation in Tibetans by regulating blood nitric oxide. GCH1通过调节血液一氧化氮参与西藏人的高海拔适应。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-18 DOI: 10.1016/j.jgg.2025.04.005
Yongbo Guo, Wangshan Zheng, Tian Yue, Baimakangzhuo, Xuebin Qi, Kai Liu, Liya Li, Yaoxi He, Bing Su
{"title":"GCH1 contributes to high-altitude adaptation in Tibetans by regulating blood nitric oxide.","authors":"Yongbo Guo, Wangshan Zheng, Tian Yue, Baimakangzhuo, Xuebin Qi, Kai Liu, Liya Li, Yaoxi He, Bing Su","doi":"10.1016/j.jgg.2025.04.005","DOIUrl":"10.1016/j.jgg.2025.04.005","url":null,"abstract":"<p><p>Nitric oxide (NO) is a key vasodilator that regulates vascular pressure and blood flow. Tibetans have developed a \"blunted\" mechanism for regulating NO levels at high altitude, with GTP cyclohydrolase 1 (GCH1) identified as a key candidate gene. Here, we present comprehensive genetic and functional analyses of GCH1, which exhibits strong Darwinian positive selection in Tibetans. We show that Tibetan-enriched GCH1 variants down-regulate its expression in the blood of Tibetans. Based on this observation, we generate the heterozygous Gch1 knockout (Gch1<sup>+</sup><sup>/</sup><sup>-</sup>) mouse model to simulate its downregulation in Tibetans. We find that under prolonged hypoxia, the Gch1<sup>+</sup><sup>/</sup><sup>-</sup> mice have relatively higher blood NO and blood oxygen saturation levels compared with the wild-type (WT) controls, providing better oxygen supplies to the cardiovascular and pulmonary systems. Markedly, hypoxia-induced cardiac hypertrophy and pulmonary remodeling are significantly attenuated in the Gch1<sup>+</sup><sup>/</sup><sup>-</sup> mice compared with the WT controls, likely due to the adaptive changes in molecular regulations related to metabolism, inflammation, circadian rhythm, extracellular matrix, and oxidative stress. This study sheds light on the role of GCH1 in regulating blood NO, contributing to the physiological adaptation of the cardiovascular and pulmonary systems in Tibetans at high altitude.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Loss of lims1 causes aberrant cardiac remodeling and heart failure via activating gp130/Jak1/Stat3 pathway in zebrafish. 在斑马鱼中,lim1的缺失通过激活gp130/Jak1/Stat3通路导致心脏重构异常和心力衰竭。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-17 DOI: 10.1016/j.jgg.2025.04.003
Wuming Qin, Xiaobo Yang, Lu Zhang, Linghui Cao, Shi Ouyang, Dafeng Yang, Yangzhao Zhou, Anji Chen, Tao Liao, Xinyu Zhu, Yuting Liu, Wei Tang, Tongtong Ma, Yiyue Tang, Yonghe Ding, Yun Deng
{"title":"Loss of lims1 causes aberrant cardiac remodeling and heart failure via activating gp130/Jak1/Stat3 pathway in zebrafish.","authors":"Wuming Qin, Xiaobo Yang, Lu Zhang, Linghui Cao, Shi Ouyang, Dafeng Yang, Yangzhao Zhou, Anji Chen, Tao Liao, Xinyu Zhu, Yuting Liu, Wei Tang, Tongtong Ma, Yiyue Tang, Yonghe Ding, Yun Deng","doi":"10.1016/j.jgg.2025.04.003","DOIUrl":"10.1016/j.jgg.2025.04.003","url":null,"abstract":"<p><p>LIM zinc finger domain containing 1 (LIMS1), an evolutionally conserved LIM domain adaptor protein, is implicated in diverse pathologies, including cancer and neurological disorders. However, its roles in cardiac diseases and the underlying mechanisms remain unclear. Here, we explore the functions and mechanisms of LIMS1 in cardiac remodeling and heart failure. We identify the elevated LIMS1 expression in patients with dilated cardiomyopathy and murine cardiomyocytes, suggesting that LIMS1 dysregulation contributes to cardiac pathology. Using CRISPR/Cas9 technology, we generate a zebrafish model of lims1 loss-of-function mutant, which exhibits severe cardiac chamber remodeling, systolic dysfunction, and premature mortality, demonstrating the essential role of lims1 in maintaining cardiac integrity. Transcriptomic profiling reveals the activation of the gp130/Jak1/Stat3 signaling in the lims1-deficient hearts. Strikingly, pharmacological inhibition of Stat3 or c-Fos partially rescues cardiomyopathy phenotypes. Our findings reveal the underlying mechanism of lims1 deficiency-caused heart failure through gp130/Jak1/Stat3 hyperactivation, offering insights into cardiac remodeling and potential therapeutic strategies.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Deep sequencing reveals SLC35A2 somatic variants in MOGHE: molecular and clinical insights. 深度测序揭示了MOGHE中SLC35A2体细胞变异:分子和临床见解。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-10 DOI: 10.1016/j.jgg.2025.04.002
Huaxia Luo, Xiaoqin Ruan, Xianyu Liu, Qingzhu Liu, Yu Sun, Yao Wang, Jixin Zhang, Lixin Cai, Yuwu Jiang, Ye Wu
{"title":"Deep sequencing reveals SLC35A2 somatic variants in MOGHE: molecular and clinical insights.","authors":"Huaxia Luo, Xiaoqin Ruan, Xianyu Liu, Qingzhu Liu, Yu Sun, Yao Wang, Jixin Zhang, Lixin Cai, Yuwu Jiang, Ye Wu","doi":"10.1016/j.jgg.2025.04.002","DOIUrl":"10.1016/j.jgg.2025.04.002","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity. 综合基因组学和转录组学分析揭示了山楂果皮颜色和种子硬度多样性的遗传和分子机制。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-04-10 DOI: 10.1016/j.jgg.2025.04.001
Jiaxin Meng, Yan Wang, Rongkun Guo, Jianyi Liu, Kerui Jing, Jiaqi Zuo, Yanping Yuan, Fengchao Jiang, Ningguang Dong
{"title":"Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity.","authors":"Jiaxin Meng, Yan Wang, Rongkun Guo, Jianyi Liu, Kerui Jing, Jiaqi Zuo, Yanping Yuan, Fengchao Jiang, Ningguang Dong","doi":"10.1016/j.jgg.2025.04.001","DOIUrl":"10.1016/j.jgg.2025.04.001","url":null,"abstract":"<p><p>Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida \"Jinruyi\" (JRY) and the soft-seed, red-peel C. pinnatifida \"Ruanzi\" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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