iDog: A multi-omics Resource for Canids Study
The domestic dog is among the most genetically diverse species and serves as a vital animal model for studying human genetic diseases. In recent years, the rapid growth of canine genomics, transcriptomics, epigenomics, and phenomics data has provided a rich foundation for research on aspects such as the domestication process, behavioral patterns, and morphological development in dogs. iDog is committed to providing comprehensive data services and online analysis tools for researchers engaged in canine studies. Since its release in 2019, iDog has been widely utilized in functional genomics research and has made significant contributions to studies on canine diseases and population genetics.
Recently, a research team led by ZHAO Wenming from the Beijing Insititute of Genomics of Chinese Academy of Sciences (National Bioinformatics Center), in collaboration with LIU Yanhu et al from the Kunming Institute of Zoology of Chinese Academy of Sciences, has launched the iDog 2.0 database. This enhanced platform provides a more comprehensive collection of multi-omics data and a broader range of online analysis tools, providing high-quality resources for the global canine research community. This work entitled “iDog: a multi-omics resource for canids study” was published online in the journal Nucleic Acid Research on November 11.
iDog 2.0 comprehensively integrates and analyzes multi-omics data resources for canines. At the genomic variation level, iDog 2.0 has collected 29.55 million single nucleotide polymorphisms (SNPs) and 16.54 million insertions/deletions (InDels) from 1 929 modern samples, as well as 29.09 million SNPs from 111 ancient Canis samples. Additionally, 43 487 breed-specific SNPs and 530 disease/trait-associated variants have been identified and integrated, providing valuable genetic information for global canine research. At the gene expression level, the platform has integrated and analyzed gene expression data from 2 947 samples, offering gene expression profiles for different canine breeds and tissues, along with differential gene expression information for various canine diseases. The platform also provides a single-cell transcriptome module containing data from 105 057 Beagle hippocampus cells. At the epigenomic level, iDog 2.0 offers DNA methylation information from 547 samples and chromatin accessibility data from 87 samples, supporting the analysis of gene expression regulation in canines. Furthermore, it provides phenotypic data for 897 dog diseases, 3 207 genotype-to-phenotype (G2P) pairs, and 349 dog disease-associated genes, along with two newly constructed ontologies for breed and disease standardization. Finally, iDog 2.0 also offers 13 online analysis tools, including the Retrieval-Augmented Generation search tool (DogRAG) and the visual breed classification tool (DogVC), to facilitate canine research for scientists.
Overview of data content and organization in iDog 2.0（Image by ZHAO Wenming's group）
