PeanutOmics: A comprehensive platform with an integrative multi-omics atlas for peanut research

Peanut (Arachis hypogaea) is an economically important legume crop, but a comprehensive understanding of its gene expression dynamics across developmental stages remains limited. To address this gap, we constructed an integrative multi-omics atlas spanning transcriptomic, proteomic, and metabolomic profiles across 22 primary vegetative and reproductive tissues. We identified 53 030 expressed genes at the transcript level, 12 826 with protein evidence, and 2035 metabolites. Among these, 2147 genes encode novel proteins, and 274 produce microproteins. Functional analyses identified WDR13, TANGO, RPP13, DEF3, SLR1-BP, and SLE2 as key genes involved in development and stress responses. Co-expression analysis grouped genes into 24 modules, many of which exhibited tissue-specific expression patterns. Pathway enrichment and correlation network analyses further highlighted the critical roles of the IAA and ARF gene families in hormone signaling and cell growth, particularly in peg development. To facilitate data accessibility and downstream research, we developed PeanutOmics (https://cgm.sjtu.edu.cn/PeanutOmics), a user-friendly web platform that integrates multi-omics datasets with advanced analytical tools. This atlas offers a valuable resource for understanding gene and metabolite regulation in peanut and lays the groundwork for advanced molecular breeding to improve crop productivity.