Towards a better understanding of the bacterial pan-genome

Abstract

The bacterial pan-genome is a relatively new concept that refers to the number of genes observed in a given set of bacterial genome sequences, either at the intra- or inter-species level. Determining the pan-genome of a given species of bacteria using a large number of strains allows one to compare multiple genes and to determine evolutionary links between isolates. This information can help to determine population structure, diversity in terms of prevalence in a given environment and pathogenicity of microorganisms. Within this review, we explain the most important issues related to pan-genome studies. We also include a brief description of some selected bacterial pan-genomes. Finally, we propose an easy-toperform workflow to study bacterial pan-genomes that will facilitate nonexperts in a pan-genome-based investigation.

Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs

“…Based on rapid advances in sequencing technologies and computational approaches in the past two decades, the classification of bacterial genes into homologous groups based on their presence or absence has become a common comparative task referred to as microbial pangenomics (Mira et al 2010;Gmiter et al 2021;Medini et al 2005). Today, researchers have access to various tools (Vernikos 2020) to input genomes or genes to define accessory and core genes or, at an even finer granularity, shell, cloud, and persistent genes.…”