PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

<jats:title>Abstract</jats:title> <jats:p> PanGBank ( <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://pangbank.genoscope.cns.fr">https://pangbank.genoscope.cns.fr</jats:ext-link> ) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering more than 4,600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393,000 genomes: GTDB all, maximizing taxonomic and environmental diversity through the inclusion of MAGs and SAGs, and GTDB refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface (PanGBank-cli), and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants. </jats:p> <jats:sec> <jats:title>Graphical Abstract</jats:title> <jats:fig id="ufig1" position="float" fig-type="figure" orientation="portrait"> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="742796v1_ufig1" position="float" orientation="portrait"/> </jats:fig> </jats:sec>