Journal of Genetics and Genomics

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Multifaceted interplays between the essential players and lipid peroxidation in ferroptosis

Conghe Liu, Zhihao Liu, Zheng Dong, Sijin Liu, Haidong Kan, Shuping Zhang

2025, 52(9): 1071-1081. doi: 10.1016/j.jgg.2025.01.009

[摘要](60)

摘要:
Ferroptosis, a type of programmed cell death, represents a distinct paradigm in cell biology. It is characterized by the iron-dependent accumulation of reactive oxygen species, which induce lipid peroxidation (LPO), and is orchestrated by the interplay between iron, lipid peroxides, and glutathione. In this review, we emphasize the frequently overlooked role of iron in LPO beyond the classical iron-driven Fenton reaction in several crucial processes that regulate cellular iron homeostasis, including iron intake and export as well as ferritinophagy, and the emerging roles of endoplasmic reticulum-resident flavoprotein oxidoreductases, especially P450 oxidoreductases, in modulating LPO. We summarize how various types of fatty acids (FAs), including saturated, monounsaturated, and polyunsaturated FAs, differentially influence ferroptosis when incorporated into phospholipids. Furthermore, we highlight the therapeutic potential of targeting LPO to mitigate ferroptosis and discuss the regulatory mechanisms of endogenous lipophilic radical-trapping antioxidants that confer resistance to ferroptosis, shedding light on therapeutic avenues for ferroptosis-associated diseases.

Enhancing crop yields to ensure food security by optimizing photosynthesis

Chunrong Li, Xuejia Du, Cuimin Liu

2025, 52(9): 1082-1095. doi: 10.1016/j.jgg.2025.01.002

[摘要](12)

摘要:
The crop yields achieved through traditional plant breeding techniques appear to be nearing a plateau. Therefore, it is essential to accelerate advancements in photosynthesis, the fundamental process by which plants convert light energy into chemical energy, to further enhance crop yields. Research focused on improving photosynthesis holds significant promise for increasing sustainable agricultural productivity and addressing challenges related to global food security. This review examines the latest advancements and strategies aimed at boosting crop yields by enhancing photosynthetic efficiency. There has been a linear increase in yield over the years in historically released germplasm selected through traditional breeding methods, and this increase is accompanied by improved photosynthesis. We explore various aspects of the light reactions designed to enhance crop yield, including light harvest efficiency through smart canopy systems, expanding the absorbed light spectrum to include far-red light, optimizing non-photochemical quenching, and accelerating electron transport flux. At the same time, we investigate carbon reactions that can enhance crop yield, such as manipulating Rubisco activity, improving the Calvin-Benson-Bassham cycle, introducing CO₂ concentrating mechanisms in C₃ plants, and optimizing carbon allocation. These strategies could significantly impact crop yield enhancement and help bridge the yield gap.

Evolutionary divergence on the Qinghai–Xizang Plateau: How life-history traits shape the diversity of plateau zokor and pika populations

Yunyang Wei, Tao Zhang, Zifeng Li, Qinyang Hua, Liduo Yin, Menglong Lei, Shilei Zhao, Shanshan Gu, Xin Zhang, Hao He, Xuemei Lu

2025, 52(9): 1096-1108. doi: 10.1016/j.jgg.2025.04.019

[摘要](0) [PDF 2118KB](1)

摘要:
Understanding how species diverge and adapt is fundamental to unraveling biodiversity. While environmental impacts on species evolution are well-documented, the roles of intrinsic life-history traits remain underexplored. The Qinghai–Xizang Plateau, with its harsh conditions and unique biodiversity, offers a natural laboratory for such investigations. Here, we examine two sympatric small mammals—the solitary, low-dispersal plateau zokor (Eospalax baileyi) and the social, high-dispersal plateau pika (Ochotona curzoniae)—to elucidate how life-history traits shape population structures and adaptive strategies. Through whole-genome sequencing and cardiac-blood phenotype analyses, we reveal striking differences in their evolutionary trajectories. Despite enduring similar environmental pressures, plateau zokor populations exhibit pronounced genetic subdivisions, high inbreeding, and distinct local adaptations. In contrast, plateau pika populations display genetic panmixia, widespread diversity, and adaptive uniformity. Demographic inference highlights that plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods, underscoring the impact of dispersal capacity on evolutionary outcomes. Our findings demonstrate that intrinsic biological traits, particularly dispersal ability, fundamentally influence genetic architecture, population connectivity, and local adaptation. This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but also offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.

Genomic predictions of invasiveness and adaptability of the cotton bollworm in response to climate change

Qi Xu, Minghui Jin, Hua Xiao, Yan Peng, Fan Zhang, Hongran Li, Kongming Wu, Yutao Xiao

2025, 52(9): 1109-1120. doi: 10.1016/j.jgg.2025.01.016

[摘要](23)

摘要:
Agricultural pests cause enormous losses in annual agricultural production. Understanding the evolutionary responses and adaptive capacity of agricultural pests under climate change is crucial for establishing sustainable and environmentally friendly agricultural pest management. In this study, we integrate climate modeling and landscape genomics to investigate the distributional dynamics of the cotton bollworm (Helicoverpa armigera) in the adaptation to local environments and resilience to future climate change. Notably, the predicted inhabitable areas with higher suitability for the cotton bollworm could be eight times larger in the coming decades. Climate change is one of the factors driving the dynamics of distribution and population differentiation of the cotton bollworm. Approximately 19,000 years ago, the cotton bollworm expanded from its ancestral African population, followed by gradual occupations of the European, Asian, Oceanian, and American continents. Furthermore, we identify seven subpopulations with high dispersal and adaptability which may have an increased risk of invasion potential. Additionally, a large number of candidate genes and SNPs linked to climatic adaptation were mapped. These findings could inform sustainable pest management strategies in the face of climate change, aiding future pest forecasting and management planning.

Resolving the spatial and cellular architecture of intra-tumor heterogeneity by multi-region dissection of lung adenocarcinoma

Song Mei, Xiaolei Wang, Mengmeng Zhao, Qing Huang, Yixuan Huang, Mingming Su, Xinlei Zhang, Xu Wang, Xueyu Hao, Tianning Wang, Yanhua Wu, Yuanhui Ma, Jingnan Wang, Peng Zhang, Yan Zheng

2025, 52(9): 1121-1132. doi: 10.1016/j.jgg.2025.02.006

[摘要](0)

摘要:
Although the spatial characteristics within the tumor microenvironment of lung adenocarcinoma (LUAD) have been identified, the mechanisms by which these factors promote LUAD progression and immune evasion remain unclear. Using spatial transcriptomics and single-cell RNA-sequencing data from multi-regional LUAD biopsies consisting of tumor core, tumor edge, and normal area, we sought to delineate the spatial heterogeneity and driving factors of cell colocalization. Two cancer cell sub-clusters (Cancer_c1 and Cancer_c2), associated with LUAD initiation and metastasis, respectively, exhibit distinct spatial distributions and immune cell colocalizations. In particular, Cancer_c1, enriched within the tumor core, could directly interact with B cells or indirectly recruit B cells through macrophages. Conversely, Cancer_c2 enriched within the tumor edge exhibits colocalization with CD8⁺ T cells. Collectively, our work elucidates the spatial distribution of cancer cell subtypes and their interaction with immune cells in the core and edge of LUAD, providing insights for developing therapeutic strategies for cancer intervention.

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

Yanhong Wu, Yuhan Fan, Yuxin Miao, Yuman Li, Guifang Du, Zeyu Chen, Jinmei Diao, Yu-Ann Chen, Mingli Ye, Renke You, Amin Chen, Yixin Chen, Wenrui Li, Wenbo Guo, Jiahong Dong, Xuegong Zhang, Yunfang Wang, Jin Gu

2025, 52(9): 1133-1147. doi: 10.1016/j.jgg.2025.01.017

[摘要](28)

摘要:
The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://lifeome.net/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of “variant” cellular states analogous to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the “deviated” states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte “intermediate” states significantly indicate poor prognosis. Besides, we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues.

Wheat TaPKL genes regulate pre-harvest sprouting and yield-related traits

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

2025, 52(9): 1148-1150. doi: 10.1016/j.jgg.2025.04.011

[摘要](22)

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Near-gapless telomere-to-telomere reference nuclear genome and variable mitochondrial genome of Amborella trichopoda

Zhonglong Guo, Jing-Fang Guo, Zhi-Yan Wei, Ren-Gang Zhang, Scott McMahan, Shuai Nie, Xue-Mei Yan, Shan-Shan Zhou, Quan-Zheng Yun, Jia-Yi Wu, Jing Ge, Yong Yang, Jia-Yu Xue, Jian-Feng Mao

2025, 52(9): 1151-1154. doi: 10.1016/j.jgg.2025.04.016

[摘要](55)

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