Over the last eight years, the volume of whole genome, gene expression, SNP genotyping, and phenotype data generated by the cotton research community has exponentially increased. The efficient utilization/re-utilization of these complex and large datasets for knowledge discovery, translation, and application in crop improvement requires them to be curated, integrated with other types of data, and made available for access and analysis through efficient online search tools. Initiated in 2012, CottonGen is an online community database providing access to integrated peer-reviewed cotton genomic, genetic, and breeding data, and analysis tools. Used by cotton researchers worldwide, and managed by experts with crop-specific knowledge, it continuous to be the logical choice to integrate new data and provide necessary interfaces for information retrieval. The repository in CottonGen contains colleague, gene, genome, genotype, germplasm, map, marker, metabolite, phenotype, publication, QTL, species, transcriptome, and trait data curated by the CottonGen team. The number of data entries housed in CottonGen has increased dramatically, for example, since 2014 there has been an 18-fold increase in genes/mRNAs, a 23-fold increase in whole genomes, and a 372-fold increase in genotype data. New tools include a genetic map viewer, a genome browser, a synteny viewer, a metabolite pathways browser, sequence retrieval, BLAST, and a breeding information management system (BIMS), as well as various search pages for new data types. CottonGen serves as the home to the International Cotton Genome Initiative, managing its elections and serving as a communication and coordination hub for the community. With its extensive curation and integration of data and online tools, CottonGen will continue to facilitate utilization of its critical resources to empower research for cotton crop improvement.

CottonGen (https://www.cottongen.org) serves as an integrated genomics platform for the cotton research community, combining comprehensive data storage with sophisticated analysis tools built on the Tripal framework. Since its establishment in 2012, CottonGen has consolidated and expanded resources previously scattered across CottonDB and the Cotton Marker Database while developing advanced analytical capabilities. The platform has expanded substantially between 2021 and 2025, with tetraploid genome assemblies and gene annotations increasing 3-fold, genotype datasets doubling, and phenotype records growing 1.8-fold. Recent developments include enhanced search and visualization capabilities through updated Map Viewer and Breeding Information Management System tools, integration of genome-wide association studies and gene expression analysis via new Tripal modules, and implementation of Genotype Investigator for Genome-Wide Analyses for interactive large-scale genotyping data exploration. Beyond data storage, CottonGen provides integrated analysis workflows spanning sequence similarity searches, synteny analysis, expression profiling, marker-trait association studies, and breeding data management. These capabilities support diverse research applications from comparative genomics and gene discovery to marker-assisted selection and cultivar development. As the official platform for the International Cotton Genome Initiative, CottonGen helps coordinate global cotton research efforts and maintains a comprehensive, actively curated resource that evolves with community research priorities.