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

Abstract

PanGBank (https://pangbank.genoscope.cns.fr) 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. Graphical Abstract