The RodentGPOmics Atlas: a comprehensive database of rodent biology for genomes and pathogens

Abstract

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.