Jiang Zhiwen, Yan Ziqing, Hou Yali, Tang Jia, Zheng Mengdi, Lu Meng, Ji Xiang, Gangavarapu Karthik, Li Xinxin, Su Shuo
Sanya Institute of Nanjing Agricultural University, Sanya 572054, China.
Academy for Advanced Interdisciplinary Studies, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Nucleic Acids Res. 2025 Jan 6;53(D1):D1144-D1150. doi: 10.1093/nar/gkae1074.
Rodents represent the most abundant order of mammals, exhibiting remarkable diversity in morphology, habitats, behaviors, and hosted pathogens. Significant attention is currently focused on rodents as experimental animals for biomedical research. However, numerous aspects of rodents remain unexplored, such as their potential in unconventional biomedical models, molecular underpinnings of intriguing complex phenotypes, adaptations to environment or climate change, and host-pathogen interactions and arms race evolution. These challenges require a systematic framework to integrate the genomic variations among rodents with information on rodent-borne pathogens. To address this gap, we have established a comprehensive, freely accessible, and user-friendly atlas named Rodent Genome and Pathogen multi-Omics (RodentGPOmics), which provides comparative analysis of rodent genomes and information on zoonotic pathogen sequences in rodents. The RodentGPOmics Atlas provides: (i) basic information on 2706 rodent species; (ii) chromosome-level visualization of genomes, functional annotations, and genomic comparisons across 121 rodent species; (iii) epidemiological profiles based on 21 852 pathogen sequences reported in rodents and (iv) a few genomic tools for in-depth exploration of rodent multi-omics. This resource aims to advance the development of biomedical models for humans for promoting public health, as well as innovate the genetics, genomics, and molecular evolution in rodents, and offer valuable knowledge on rodent-borne emerging/re-emerging zoonotic infectious diseases. The resources are freely available and easy-to-use at http://RodentGPOmics.njau.edu.cn:8888/Rodent/index/homePage.
啮齿动物是哺乳动物中数量最多的目，在形态、栖息地、行为和携带的病原体方面表现出显著的多样性。目前，啮齿动物作为生物医学研究的实验动物受到了广泛关注。然而，啮齿动物的许多方面仍未被探索，例如它们在非传统生物医学模型中的潜力、有趣复杂表型的分子基础、对环境或气候变化的适应，以及宿主与病原体的相互作用和军备竞赛进化。这些挑战需要一个系统的框架，将啮齿动物之间的基因组变异与啮齿动物传播病原体的信息整合起来。为了填补这一空白，我们建立了一个全面、免费访问且用户友好的图谱，名为啮齿动物基因组与病原体多组学图谱（RodentGPOmics），它提供了啮齿动物基因组的比较分析以及啮齿动物中人畜共患病原体序列的信息。啮齿动物基因组与病原体多组学图谱提供：（i）2706种啮齿动物的基本信息；（ii）121种啮齿动物基因组的染色体水平可视化、功能注释和基因组比较；（iii）基于啮齿动物中报告的21852个病原体序列的流行病学概况；以及（iv）一些用于深入探索啮齿动物多组学的基因组工具。该资源旨在推动人类生物医学模型的发展以促进公共卫生，同时创新啮齿动物的遗传学、基因组学和分子进化，并提供有关啮齿动物传播的新出现/再次出现的人畜共患传染病的宝贵知识。这些资源可在http://RodentGPOmics.njau.edu.cn:8888/Rodent/index/homePage免费获取且易于使用。
