Journal of Genetics and Genomics

Deciphering the influence of gut and oral microbiomes on menopause for healthy aging

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

2025, 52(5): 601-614. doi: 10.1016/j.jgg.2024.11.010

Abstract (2)

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.

Advances in plant oxygen sensing: endogenous and exogenous mechanisms

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

2025, 52(5): 615-627. doi: 10.1016/j.jgg.2024.11.014

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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.

The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance

Alex Z. Zaccaron, Ioannis Stergiopoulos

2025, 52(5): 628-640. doi: 10.1016/j.jgg.2024.10.010

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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.

Revealing extensive inbreeding and less efficient purging of deleterious mutations in wild Amur tigers in China

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

2025, 52(5): 641-649. doi: 10.1016/j.jgg.2024.12.004

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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 (F_ROH = 0.50) than in captive individuals (F_ROH = 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.

Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus

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

2025, 52(5): 650-665. doi: 10.1016/j.jgg.2024.12.003

Abstract (0)

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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.

Znf706 regulates germ plasm assembly and primordial germ cell development in zebrafish

Weiying Zhang, Yaqi Li, Han Li, Xin Liu, Tao Zheng, Guangyuan Li, Boqi Liu, Tong Lv, Zihang Wei, Cencan Xing, Shunji Jia, Anming Meng, Xiaotong Wu

2025, 52(5): 666-679. doi: 10.1016/j.jgg.2024.11.007

Abstract (0)

Abstract:
The cell fate of primordial germ cell (PGC) in zebrafish is pre-determined by maternally deposited germ plasm, which is packaged into ribonucleoprotein complex in oocytes and inherited into PGC-fated cells in embryos. However, the maternal factors regulating the assembly of germ plasm and PGC development remain poorly understood. In this study, we report that the maternal transcription factor Znf706 regulates the assembly of germ plasm factors into a granule-like structure localized perinuclearly in PGC during migration. Maternal and zygotic mutants of znf706 exhibit deficient germ plasm scattering at the early embryonic stage, decreased PGC numbers with some mislocation during PGC migration, and a lower female ratio in adulthood. Notably, the implementation of Znf706 CUT&Tag and RNA-seq on immature oocytes uncovers that Znf706 in stage I oocytes may promote transcription of several mitochondrial genes in addition to other functions. Hence, we propose that Znf706 is implicated in germ plasm assembly and PGC development in zebrafish.

Foxo1 directs the transdifferentiation of mouse Sertoli cells into granulosa-like cells

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

2025, 52(5): 680-688. doi: 10.1016/j.jgg.2024.12.006

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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.

KanCell: dissecting cellular heterogeneity in biological tissues through integrated single-cell and spatial transcriptomics

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

2025, 52(5): 689-705. doi: 10.1016/j.jgg.2024.11.009

Abstract (2)

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.

Identification and functional characterization of pathogenic FOXI3 variants in craniofacial microsomia

Xin Chen, Ying Chen, Chenlong Li, Run Yang, Yiyuan Chen, Tianyu Zhang, Yaying Zhu, Jing Ma

2025, 52(5): 706-709. doi: 10.1016/j.jgg.2025.02.010

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The Cys2/His2 type zinc finger protein TaZFP21 functions as a repressor of drought response in wheat

Yongliang Li, Zhenbing Ma, Ming Yu, Qiannan Wang, You Li, Shunxing Ye, Wenjun Xiao, Shuai Jiang, Xiaoxiao Zou, Hude Mao, Xinhong Guo

2025, 52(5): 710-713. doi: 10.1016/j.jgg.2025.03.007

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A critical evaluation of deep-learning based phylogenetic inference programs using simulated datasets

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

2025, 52(5): 714-717. doi: 10.1016/j.jgg.2025.01.006

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2025 Vol. 52, No. 5