Current Articles

2025, Volume 52,  Issue 11

Commentary
Solving the puzzle of salicylic acid biosynthesis in plants
Pei Miao, Jian-Min Zhou
2025, 52(11): 1305-1307. doi: 10.1016/j.jgg.2025.08.003
Abstract:
Original Research
A telomere-to-telomere genome assembly of the large yellow croaker provides insights into evolution of golden-yellow coloration
Shengyong Xu, Qi Liu, Tianyan Yang, Zhiqiang Han
2025, 52(11): 1401-1412. doi: 10.1016/j.jgg.2025.09.006
Abstract:
The large yellow croaker (Larimichthys crocea) is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration. However, the genetic mechanisms underlying golden-yellow coloration remain unclear. Here, we construct a telomere-to-telomere gap-free genome assembly (T2T-Larcro_1.0) spanning 716.87 Mb, with a contig N50 of 31.75 Mb. Compared to the current reference genome (L_crocea_2.0), T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes. This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes (e.g., OPNVA, nNOS, RDH13) potentially involved in evolution of golden-yellow coloration. Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin (VA opsin) in skin tissues of the large yellow croaker, suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration. Integrating genomics and transcriptomics results, we uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change (golden-yellow to silvery-white) in L. crocea. Collectively, our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of golden-yellow coloration in L. crocea. This high-quality genome assembly also serves as an improved resource for biological evolution, genetic improvement, and selective breeding of L. crocea.
The Magnaporthe oryzae effector MoCHT1 targets and stabilizes rice OsLLB to suppress jasmonic acid synthesis and enhance infection
Ningning Shen, Chuner Lu, Yanhong Wen, Boqian Deng, Yu Dong, Xiaojun Gong, Yuhao Liu, Chengyu Liu, Zixuan Liu, Xianya Deng, Li-Bo Han, Dingzhong Tang, Yuan-Bao Li
2025, 52(11): 1387-1400. doi: 10.1016/j.jgg.2025.05.004
Abstract:
Rice blast disease caused by Magnaporthe oryzae poses a serious threat to rice security worldwide. This filamentous pathogen modulates rice defense responses by secreting effectors to facilitate infection. The phytohormone jasmonic acid (JA) plays crucial roles in the response to rice blast fungus. However, how M. oryzae disrupts JA-mediated resistance in rice is not well understood. In this study, we identify a new effector, a chloroplast-targeting protein (MoCHT1), from M. oryzae. Knocking out MoCHT1 decreases virulence, whereas heterologous expression of MoCHT1 in rice compromises disease resistance. MoCHT1 interacts with a rice LESION AND LAMINA BENDING (OsLLB) protein, a negative regulator of JA biosynthesis in the chloroplast. Loss-of-function of OsLLB leads to increased JA accumulation, thereby improving resistance to rice blast. The interaction between MoCHT1 and OsLLB results in the inhibition of OsLLB degradation, consequently reducing JA accumulation, thereby impairing JA content and decreasing plant disease resistance. Overall, this study reveals the molecular mechanism by which M. oryzae utilizes MoCHT1 to subvert rice JA signaling, broadening our understanding of how pathogens circumvent host immune responses by manipulating plant defense hormone biosynthesis.
3' untranslated region somatic variants connect alternative polyadenylation dysregulation in human cancers
Qiushi Xu, Xiaomeng Cheng, Qianru Li, Peng Yu, Xiaolan Zhou, Yu Chen, Limin Lin, Ting Ni, Zhaozhao Zhao
2025, 52(11): 1376-1386. doi: 10.1016/j.jgg.2025.03.006
Abstract:
Somatic variants in the cancer genome influence gene expression through diverse mechanisms depending on their specific locations. However, a systematic evaluation of the effects of somatic variants located in 3' untranslated regions (3' UTRs) on alternative polyadenylation (APA) of mRNA remains lacking. In this study, we analyze 10,199 tumor samples across 32 cancer types and identify 1333 somatic single nucleotide variants (SNVs) associated with abnormal 3' UTR APA. Mechanistically, these 3' UTR SNVs can alter cis-regulatory elements, such as the poly(A) signal and UGUA motif, leading to changes in APA. Minigene assays confirm that 3' UTR SNVs in multiple genes, including RPS23 and CHTOP, induce aberrant APA. Among affected genes, 62 exhibit differential stability between tandem 3' UTR isoforms, including HSPA4 and UCK2, validated by experimental assays. Finally, we establish that SNV-related abnormal APA usage serves as an additional layer of expression regulation for tumor-suppressor gene HMGN2 in breast cancer. Collectively, this study reveals 3' UTR APA as a critical mechanism mediating the functional impact of somatic noncoding variants in human cancers.
Amyloid-β oligomers drive amyloid deposit and cascaded tau pathology of Alzheimer's disease in aged brains of non-human primates
Zhengxiao He, Wenchang Zhang, Ping Chen, Siyao Li, Min Tao, Feng Yue, Wei Hong, Su Feng, Naihe Jing
2025, 52(11): 1367-1375. doi: 10.1016/j.jgg.2025.02.007
Abstract:
Alzheimer's disease (AD), the most prevalent form of dementia, disproportionately affects the elderly population. While aging is widely recognized as a major risk factor for AD, the precise mechanisms by which aging contributes to the pathogenesis of AD remain poorly understood. In our previous work, the neuropathological changes in the brains of aged cynomolgus monkeys (≥18 years old) following parenchymal cerebral injection of amyloid-β oligomers (AβOs) have been characterized. Here, we extend our investigation to middle-aged cynomolgus monkeys (≤15 years old) to establish an AD model. Surprisingly, immunohistochemical analysis reveals no detectable AD-related pathology in the brains of middle-aged monkeys, even after AβOs injection. In a comprehensive pathological analysis of 38 monkeys, we observe that the amyloid-β (Aβ) burden increases significantly with advancing age. Notably, the density of Aβ plaques is markedly higher in the ventral regions compared with the dorsal regions of aged monkey brains. Furthermore, we demonstrate that tau phosphorylation coincides with the accumulation of extensive Aβ plaques and exhibits a positive correlation with Aβ burden in aged monkeys. Collectively, these findings underscore the critical role of the aged brain in providing the necessary conditions for AβO-induced AD pathologies in cynomolgus monkeys.
Research Communications
Proximity labeling proteomics with cilia-TurboID transgenic mice identified regulators of motile cilia function
Pan Wang, Xiangnan Wu, Liqing Xiao, Qingru Yu, Yan Peng, Mengting Yan, Jun Tang, Mingqiang Hu, Hongtao Li, Li Li, Lingfei Luo, Ming Ma
2025, 52(11): 1413-1416. doi: 10.1016/j.jgg.2025.07.013
Abstract (139)
Abstract:
A gap-free and haplotype-resolved genome of an early-season indica variety provides insights into rice thermotolerance and grain quality
Wenjing Tao, Leilei Qiu, Jingsheng Zheng, Liangrong Jiang, Qiwen Xu, Shaowei Xu, Shiting Song, Zhibiao Fan, Qixin Zheng, Qinqin Wu, Jiupan Han, Rui Li, Jingxian Wang, Yuchao Cui, Xi Huang, Changlin Zheng, Hai Zhang, Rongyu Huang, Xinhao Ouyang
2025, 52(11): 1417-1420. doi: 10.1016/j.jgg.2025.04.020
Abstract:
Review
The circadian clock at the intersection of metabolism and aging – emerging roles of metabolites
Yue Dong, Sin Man Lam, Yan Li, Min-Dian Li, Guanghou Shui
2025, 52(11): 1325-1336. doi: 10.1016/j.jgg.2025.04.014
Abstract:
The circadian clock is a highly hierarchical network of endogenous pacemakers that primarily maintains and directs oscillations through transcriptional and translational feedback loops, which modulates an approximately 24-h cycle of endocrine and metabolic rhythms within cells and tissues. While circadian clocks regulate metabolic processes and related physiology, emerging evidence indicates that metabolism and circadian rhythm are intimately intertwined. In this review, we highlight the concept of metabolites, including lipids and other polar metabolites generated from intestinal microbial metabolism and nutrient intake, as time cues that drive changes in circadian rhythms, which in turn influence metabolism and aging. Furthermore, we discuss the roles of functional metabolites as circadian cues, paving a new direction on potential intervention targets of circadian disruption, pathological aging, as well as metabolic diseases that are clinically important.
New insights into plant cell wall functions
Lanjun Zhang, Chengxu Gao, Yihong Gao, Hanlei Yang, Meiru Jia, Xiaohong Wang, Baocai Zhang, Yihua Zhou
2025, 52(11): 1308-1324. doi: 10.1016/j.jgg.2025.04.013
Abstract:
The plant cell wall is an extremely complicated natural nanoscale structure composed of cellulose microfibrils embedded in a matrix of noncellulosic polysaccharides, further reinforced by the phenolic compound lignins in some cell types. Such a network formed by the interactions of multiscale polymers actually reflects functional form of the cell wall to meet the requirements of plant cell functionalization. Therefore, how plants assemble cell wall functional structure is fundamental in plant biology and critical for crop trait formation and domestication as well. Due to the lack of effective analytical techniques to characterize this fundamental but complex network, it remains difficult to establish direct links between cell-wall genes and phenotypes. The roles of plant cell walls are often underestimated as indirect. Over the past decades, many genes involved in cell wall biosynthesis, modification, and remodeling have been identified. The application of a variety of state-of-the-art techniques has made it possible to reveal the fine cell wall networks and polymer interactions. Hence, many exciting advances in cell wall biology have been achieved in recent years. This review provides an updated overview of the mechanistic and conceptual insights in cell wall functionality, and prospects the opportunities and challenges in this field.
Understanding and enhancing rice resistance to false smut disease
De-Qiang Li, Xiao-Ling Liu, Meng Yuan, Wenxian Sun, Jian-Min Zhou, Wen-Ming Wang, Jing Fan
2025, 52(11): 1359-1366. doi: 10.1016/j.jgg.2025.03.014
Abstract:
Flower-infecting fungi have caused many economically important diseases in crop production. The fungal pathogen Ustilaginoidea virens infects developing rice florets, causing false smut disease, which leads to reduced grain yield and quality, as well as contamination with mycotoxins that pose hazards to human health and food security. To ensure rice production, substantial efforts have been made to understand the interaction between rice and U. virens. In this review, we summarize the current understanding of rice resistance mechanisms to U. virens. We discuss the evaluation of false smut resistance, quantitative resistance loci, potential defense strategies of rice panicles, pathogen effector-driven identification of resistance-related genes, and engineering of false smut resistance. We conclude by proposing an integrated defense system that includes disease avoidance, immune response, metabolic adaptation, and the inhibition of susceptibility factors. Furthermore, we outline four critical stages of interaction between rice and U. virens that are essential for understanding and enhancing organ-specific rice resistance to false smut disease.
Local trafficking and long-distance transport of small RNAs in plants
Yi Zhao, Binglian Zheng
2025, 52(11): 1347-1358. doi: 10.1016/j.jgg.2025.03.011
Abstract:
Canonical small RNAs in plants, including microRNAs and small interfering RNAs, are key triggers of RNA interference and regulate nearly every major biological process in plants. To establish systemic silencing, small RNAs undergo both short-distance intracellular trafficking or intercellular communication and long-distance transport from one organ to another, even across parasites or pathogens. This enables the delivery of effector molecules throughout the plant, promoting the spread of gene silencing. Biologically, the spatiotemporal regulation of small RNAs results in gradient distributions within cells or along the direction of organogenesis. Furthermore, the spreading capacity of small RNAs, generated in somatic or nurse cells, can guide target gene silencing in germlines in plants. In this review, we summarize recent advances in understanding the regulation and functional roles of local trafficking and long-distance transport of plant small RNAs in developmental polarity, the maintenance of cell identity, and with a particular focus, the mechanisms of small RNA movement and delivery between companion cells and gametes in plants. Additionally, we discuss the methods and challenges of monitoring small RNA transport in vivo through live imaging, as well as the potential applications of small RNA transport and delivery in the development of RNA-based pesticides.
Unlocking soybean potential: genetic resources and omics for breeding
Zongbiao Duan, Liangwei Xu, Guoan Zhou, Zhou Zhu, Xudong Wang, Yanting Shen, Xin Ma, Zhixi Tian, Chao Fang
2025, 52(11): 1337-1346. doi: 10.1016/j.jgg.2025.02.004
Abstract:
Soybean (Glycine max) is a vital foundation of global food security, providing a primary source of high-quality protein and oil for human consumption and animal feed. The rising global population has significantly increased the demand for soybeans, emphasizing the urgency of developing high-yield, stress-tolerant, and nutritionally superior cultivars. The extensive collection of soybean germplasm resources—including wild relatives, landraces, and cultivars—represents a valuable reservoir of genetic diversity critical for breeding advancements. Recent breakthroughs in genomic technologies, particularly high-throughput sequencing and multi-omics approaches, have revolutionized the identification of key genes associated with essential agronomic traits within these resources. These innovations enable precise and strategic utilization of genetic diversity, empowering breeders to integrate traits that improve yield potential, resilience to biotic and abiotic stresses, and nutritional quality. This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding. It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.