iFish: a comprehensive multi-omics database for fish genetics, transcriptional regulation, and epigenetic research

The explosive expansion of fish multi-omics data is reshaping basic and applied research in fisheries and aquaculture. Here, we introduce iFish, a rigorously curated and comprehensive resource that integrates genome, transcriptome, epigenome, and proteome datasets from 88 fish species. From 884 whole-genome sequencing datasets, we identified 137.04 million single-nucleotide polymorphisms and 45.52 million insertions/deletions. Leveraging 9797 bulk RNA-seq, 293 single-cell RNA-seq, and 840 microRNA (miRNA)-seq datasets, we quantified 1.87 million messenger RNAs, 287 873 long noncoding RNAs, 197 554 circular RNAs, and 6068 mature miRNAs across different tissues of multiple species. By integrating 1563 epigenetics sequencing datasets, we provided genome-wide maps of histone modifications, chromatin accessibility, DNA methylation, and three-dimensional chromatin interactions. Furthermore, 50 proteomics projects were included for protein expression profiling. In addition, to facilitate gene analyses, we also curated 2.7 million gene annotation entries, identified homologous genes, annotated 192 107 transcription factors (TFs), constructed TF regulatory networks and gene co-expression networks, and performed cross-species conservation analyses of noncoding RNAs. Finally, we established the iFish database (https://gonglab.hzau.edu.cn/iFish/), a user-friendly platform that supports interactive browsing, visualization, and download. With comprehensive data and useful tools, iFish will advance genetic, transcriptional-regulatory, and epigenetic investigations, and accelerate genetic improvement and practical applications in aquaculture.