Journal of Genetics and Genomics最新文献_第7页

A critical evaluation of deep-learning based phylogenetic inference programs using simulated datasets. 使用模拟数据集对基于深度学习的系统发育推断程序进行关键评估。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2025-01-15 DOI: 10.1016/j.jgg.2025.01.006

Yixiao Zhu, Yonglin Li, Chuhao Li, Xing-Xing Shen, Xiaofan Zhou

引用次数: 0

Foxo1 directs the transdifferentiation of mouse Sertoli cells into granulosa-like cells. Foxo1指导小鼠支持细胞向颗粒样细胞的转分化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2024-12-15 DOI: 10.1016/j.jgg.2024.12.006

Junhua Chen, Changhuo Cen, Mengyue Wang, Shanshan Qin, Bowen Liu, Zhiming Shen, Xiuhong Cui, Xiaohui Hou, Fei Gao, Min Chen

{"title":"Foxo1 directs the transdifferentiation of mouse Sertoli cells into granulosa-like cells.","authors":"Junhua Chen, Changhuo Cen, Mengyue Wang, Shanshan Qin, Bowen Liu, Zhiming Shen, Xiuhong Cui, Xiaohui Hou, Fei Gao, Min Chen","doi":"10.1016/j.jgg.2024.12.006","DOIUrl":"10.1016/j.jgg.2024.12.006","url":null,"abstract":"Sertoli and granulosa cells, the initial differentiated somatic cells in bipotential gonads, play crucial roles in directing male and female gonad development, respectively. The transcription factor Foxo1 is involved in diverse cellular processes, and its expression in gonadal somatic cells is sex-dependent. While Foxo1 is abundantly expressed in ovarian granulosa cells, it is notably absent in testicular Sertoli cells. Nevertheless, its function in gonadal somatic cell differentiation remains elusive. In this study, we find that ectopic expression of Foxo1 in Sertoli cells leads to defects in testes development. Further study uncovers that the ectopic expression of Foxo1 induces the abundant expression of Foxl2 in Sertoli cells, along with the upregulation of other female-specific genes. In contrast, the expression of male-specific genes is reduced. Mechanistic studies indicate that Foxo1 directly binds to the promoter region of Foxl2, inducing its expression. Our findings highlight that Foxo1 serves as a key regulator for the lineage maintenance of ovarian granulosa cells. This study contributes valuable insights into understanding the regulatory mechanisms governing the lineage maintenance of gonadal somatic cells.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"680-688"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840255","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

Advances in plant oxygen sensing: endogenous and exogenous mechanisms. 植物氧传感的研究进展：内源和外源机制。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2024-12-09 DOI: 10.1016/j.jgg.2024.11.014

Zhen Yan, Songyi Yang, Chen Lin, Jin Yan, Meng Liu, Si Tang, Weitao Jia, Jianquan Liu, Huanhuan Liu

{"title":"Advances in plant oxygen sensing: endogenous and exogenous mechanisms.","authors":"Zhen Yan, Songyi Yang, Chen Lin, Jin Yan, Meng Liu, Si Tang, Weitao Jia, Jianquan Liu, Huanhuan Liu","doi":"10.1016/j.jgg.2024.11.014","DOIUrl":"10.1016/j.jgg.2024.11.014","url":null,"abstract":"Oxygen is essential for the biochemical processes that sustain life in eukaryotic organisms. Although plants produce oxygen through photosynthesis, they often struggle to survive in low-oxygen environments, such as during flooding or submergence. To endure these conditions, they must reprogram their developmental and metabolic networks, and the adaptation process involves the continuous detection of both exogenous hypoxic signals and endogenous oxygen gradients. Recent research has significantly advanced our understanding of how plants respond to both endogenous and exogenous hypoxia signals. In this review, we explore advancements in both areas, comparing them to responses in animals, with a primary focus on how plants perceive and respond to exogenous hypoxic conditions, particularly those caused by flooding or submergence, as well as the hypoxia signaling pathways in different crops. Additionally, we discuss the interplay between endogenous and exogenous hypoxia signals in plants. Finally, we discuss future research directions aimed at improving crop resilience to flooding by integrating the perception and responses to both endogenous and exogenous signals. Through these efforts, we aspire to contribute to the development of crop varieties that are not only highly resistant but also experience minimal growth and yield penalties, thereby making substantial contributions to agricultural science.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"615-627"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787768","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

KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics. KanCell：通过集成单细胞和空间转录组学剖析生物组织中的细胞异质性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2025-01-23 DOI: 10.1016/j.jgg.2024.11.009

Zhenghui Wang, Ruoyan Dai, Mengqiu Wang, Lixin Lei, Zhiwei Zhang, Kaitai Han, Zijun Wang, Qianjin Guo

{"title":"KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics.","authors":"Zhenghui Wang, Ruoyan Dai, Mengqiu Wang, Lixin Lei, Zhiwei Zhang, Kaitai Han, Zijun Wang, Qianjin Guo","doi":"10.1016/j.jgg.2024.11.009","DOIUrl":"10.1016/j.jgg.2024.11.009","url":null,"abstract":"KanCell is a deep learning model based on Kolmogorov-Arnold networks (KAN) designed to enhance cellular heterogeneity analysis by integrating single-cell RNA sequencing and spatial transcriptomics (ST) data. ST technologies provide insights into gene expression within tissue context, revealing cellular interactions and microenvironments. To fully leverage this potential, effective computational models are crucial. We evaluate KanCell on both simulated and real datasets from technologies such as STARmap, Slide-seq, Visium, and Spatial Transcriptomics. Our results demonstrate that KanCell outperforms existing methods across metrics like PCC, SSIM, COSSIM, RMSE, JSD, ARS, and ROC, with robust performance under varying cell numbers and background noise. Real-world applications on human lymph nodes, hearts, melanoma, breast cancer, dorsolateral prefrontal cortex, and mouse embryo brains confirmed its reliability. Compared with traditional approaches, KanCell effectively captures non-linear relationships and optimizes computational efficiency through KAN, providing an accurate and efficient tool for ST. By improving data accuracy and resolving cell type composition, KanCell reveals cellular heterogeneity, clarifies disease microenvironments, and identifies therapeutic targets, addressing complex biological challenges.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"689-705"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693443","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

Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus. 转录因子 BnaC09.FUL 和 BnaC06.WIP2 在长日照条件下拮抗调控甘蓝型油菜的开花时间。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2024-12-12 DOI: 10.1016/j.jgg.2024.12.003

Yuanchang Min, Shuangcheng He, Xin Wang, Huan Hu, Shihao Wei, Ankang Ge, Lixi Jiang, Saiqi Yang, Yuan Guo, Zijin Liu, Mingxun Chen

{"title":"Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus.","authors":"Yuanchang Min, Shuangcheng He, Xin Wang, Huan Hu, Shihao Wei, Ankang Ge, Lixi Jiang, Saiqi Yang, Yuan Guo, Zijin Liu, Mingxun Chen","doi":"10.1016/j.jgg.2024.12.003","DOIUrl":"10.1016/j.jgg.2024.12.003","url":null,"abstract":"Appropriate flowering time in rapeseed (Brassica napus L.) is vital for preventing losses from weather, diseases, and pests. However, the molecular basis of its regulation remains largely unknown. Here, a genome-wide association study identifies BnaC09.FUL, a MADS-box transcription factor, as a promising candidate gene regulating flowering time in B. napus. BnaC09.FUL expression increases sharply in B. napus shoot apices near bolting. BnaC09.FUL overexpression results in early flowering, while BnaFUL mutation causes delayed flowering in B. napus. A zinc finger transcription factor, BnaC06.WIP2, is identified as an interaction partner of BnaC09.FUL, and BnaC06.WIP2 overexpression delays flowering in B. napus, with RNA sequencing revealing its influence on the expression of many flowering-associated genes. We further demonstrate that BnaC06.WIP2 directly represses the expression of BnaA05.SOC1, BnaC03.SOC1, BnaC04.SOC1, BnaC06.FT, BnaA06.LFY, BnaC07.FUL, BnaA08.CAL, and BnaC03.CAL and indirectly inhibits the expression of other flowering time-related genes. Genetic and molecular investigations highlight the antagonistic relationship between BnaC09.FUL and BnaC06.WIP2 in regulating the flowering time in B. napus through direct regulation of the expression of BnaC03.SOC1, BnaA08.CAL, and BnaC03.CAL. Overall, our findings provide a mechanism by which the BnaC09.FUL-BnaC06.WIP2 transcriptional regulatory module controls the flowering time in B. napus.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"650-665"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824889","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

Revealing extensive inbreeding and less efficient purging of deleterious mutations in wild Amur tigers in China. 揭示了中国野生阿穆尔虎广泛的近亲繁殖和对有害突变的低效清除。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2024-12-12 DOI: 10.1016/j.jgg.2024.12.004

Tianming Lan, Haimeng Li, Boyang Liu, Minhui Shi, Yinping Tian, Sunil Kumar Sahu, Liangyu Cui, Nicolas Dussex, Dan Liu, Yue Ma, Weiyao Kong, Shanlin Liu, Jiale Fan, Yue Zhao, Yuan Fu, Qiye Li, Chen Lin, Love Dalén, Huan Liu, Le Zhang, Guangshun Jiang, Yanchun Xu

{"title":"Revealing extensive inbreeding and less efficient purging of deleterious mutations in wild Amur tigers in China.","authors":"Tianming Lan, Haimeng Li, Boyang Liu, Minhui Shi, Yinping Tian, Sunil Kumar Sahu, Liangyu Cui, Nicolas Dussex, Dan Liu, Yue Ma, Weiyao Kong, Shanlin Liu, Jiale Fan, Yue Zhao, Yuan Fu, Qiye Li, Chen Lin, Love Dalén, Huan Liu, Le Zhang, Guangshun Jiang, Yanchun Xu","doi":"10.1016/j.jgg.2024.12.004","DOIUrl":"10.1016/j.jgg.2024.12.004","url":null,"abstract":"Inbreeding increases genome homozygosity within populations, which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits. In small populations, genetic purging that occurs under the pressure of natural selection acts as an opposing force, contributing to a reduction of deleterious alleles. Both inbreeding and genetic purging are paramount in the field of conservation genomics. The Amur tiger (Panthera tigris altaica) lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet. Using genome-wide assessment and comparison, we reveal substantially higher and more extensive inbreeding in wild Amur tigers (FROH = 0.50) than in captive individuals (FROH = 0.24). However, a relatively reduced number of loss-of-function mutations in wild Amur tigers is observed compared to captive individuals, indicating genetic purging of inbreeding load with relatively large-effect alleles. The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging, with purifying selection also contributing to this process. These findings provide valuable insights for the future conservation of Amur tigers.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"641-649"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824887","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

The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance. 真菌基因组组织的动态及其对宿主适应性和抗真菌性的影响。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2024-11-08 DOI: 10.1016/j.jgg.2024.10.010

Alex Z Zaccaron, Ioannis Stergiopoulos

{"title":"The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance.","authors":"Alex Z Zaccaron, Ioannis Stergiopoulos","doi":"10.1016/j.jgg.2024.10.010","DOIUrl":"10.1016/j.jgg.2024.10.010","url":null,"abstract":"Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions. In this review, we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance. We examine key features and the heterogeneity of genomes across different fungal species, including but not limited to their chromosome content, DNA composition, distribution and arrangement of their content across chromosomes, and other major traits. We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions. Fungal genomes exhibit large variations in size, gene content, and structural features, such as the abundance of transposable elements (TEs), compartmentalization into gene-rich and TE-rich regions, and the presence or absence of dispensable chromosomes. Genomic structural variations are equally diverse in fungi, ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds, to targeted deletion of effector encoding genes that may promote virulence. Finally, the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides. Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"628-640"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632885","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

Deciphering the influence of gut and oral microbiomes on menopause for healthy aging. 解读肠道和口腔微生物群对更年期的影响，促进健康老龄化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-05-01 Epub Date: 2025-01-09 DOI: 10.1016/j.jgg.2024.11.010

Shuting Yu, Feiling Huang, Yixuan Huang, Fangxu Yan, Yi Li, Shenglong Xu, Yan Zhao, Xinlei Zhang, Rong Chen, Xingming Chen, Peng Zhang

{"title":"Deciphering the influence of gut and oral microbiomes on menopause for healthy aging.","authors":"Shuting Yu, Feiling Huang, Yixuan Huang, Fangxu Yan, Yi Li, Shenglong Xu, Yan Zhao, Xinlei Zhang, Rong Chen, Xingming Chen, Peng Zhang","doi":"10.1016/j.jgg.2024.11.010","DOIUrl":"10.1016/j.jgg.2024.11.010","url":null,"abstract":"Menopause is characterized by the cessation of menstruation and a decline in reproductive function, which is an intrinsic component of the aging process. However, it has been a frequently overlooked field of women's health. The oral and gut microbiota, constituting the largest ecosystem within the human body, are important for maintaining human health and notably contribute to the healthy aging of menopausal women. Therefore, a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance. This paper presents the current understanding of the microbiome during menopause, with a particular focus on alterations in the oral and gut microbiota. Our study elucidates the complex interplay between the microbiome and sex hormone levels, explores microbial crosstalk dynamics, and investigates the associations between the microbiome and diseases linked to menopause. Additionally, this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases. Given that menopause can last for approximately 30 years, gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions, which may result in symptomatic relief from menopause and an increase in quality of life in women.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"601-614"},"PeriodicalIF":6.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693415","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

The circadian clock at the intersection of metabolism and aging - emerging roles of metabolites. 代谢与衰老交叉点的生物钟——代谢物的新作用。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-29 DOI: 10.1016/j.jgg.2025.04.014

Yue Dong, Sin Man Lam, Yan Li, Min-Dian Li, Guanghou Shui

引用次数: 0

Wheat TaPKL genes regulate pre-harvest sprouting and yield-related traits. 小麦PKL基因调控收获前发芽和产量相关性状。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-25 DOI: 10.1016/j.jgg.2025.04.011

Wanqing Bai, Ziyi Yang, Xuchang Yu, Shuxian Huang, Yufan Wang, Yexing Jing, Yunwei Zhang, Jiaqiang Sun

引用次数: 0