TomOmics: An integrative multi-omics platform for comparative and functional research in tomato

Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops and a model species for research within the Solanaceae family, holding both economic and scientific significance. Rapid progress in multi-omics technologies has transformed tomato research, generating large amounts of multi-omics data that require an efficient platform for integrated management and analysis. However, existing databases face challenges in effectively identifying genes of interest and supporting comparative studies across diverse cultivars and germplasm resources. To address these limitations, we developed the Tomato Multi-Omics Platform (TomOmics, http://tomatogenetics.cau.edu.cn), a comprehensive resource that integrates a wealth of multi-omics datasets, including genomics, variomics, transcriptomics, epigenomics, phenomics, and metabolomics from tomato and its closely related species. This platform encompasses multiple reference genomes, millions of annotated genes supported by diverse functional databases, extensive transcriptome data spanning multiple tissues and developmental stages, DNA methylation signals, as well as substantial genetic variants and metabolites. Leveraging these integrated resources, TomOmics was established as a comprehensive platform for pan-genome, comparative genomics, and transcriptome analysis specifically tailored to tomato research. Furthermore, it provides a multi-omics integration interface and a suite of user-friendly tools designed to support a wide range of customized bioinformatic analyses. TomOmics will serve as a valuable resource for advancing functional genomics studies and facilitating genetic breeding in tomato.