The grammar of the pangenome: terms, concepts, methods, and emerging patterns—a general framework for comparative genomics and genome biology

The concept of the pangenome has emerged as the approach of choice for targeted comparative genomics across groups of organisms, from strain or population levels within a species to broader taxonomic or phenotypic categories. Pangenome analyses employ diverse procedures that inevitably introduce reproducibility challenges. Nevertheless, they have already yielded important insights into the structure, function, and evolution of archaeal, bacterial, and eukaryotic genomes across space, time, biogeography, and phylogeny. There is a wide range of applications from vaccine design to synthetic biology that are expected to yield additional technological and biomedical tools for genome biology and biotechnology. We review here the basic concepts underpinning pangenome research, including the estimation of gene and protein family numbers, the modeling of open and closed pangenomes, and key definitions relevant to reporting guidelines. We list and compare computational platforms, algorithms, and data structures, along with their salient features. We present key findings from 249 taxa covering 17,858 genome sequences, subjected to such analyses, and discuss major patterns observed, such as novel families per genome and pangenome size estimates for this validated data set. We propose revised criteria for pangenomes, standard operating procedures, and further targets to enhance the reproducibility of analysis and expand opportunities for experimental and computational comparative genomics. This framework attempts to clarify current methodologies and chart a path forward for integrating pangenome analyses