Challenges in prokaryote pangenomics

Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error- prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.

Automated summary

Horizontal gene transfer (HGT) and patterns of gene gain and loss are essential in bacterial evolution. Understanding these patterns can shed light on selection's role in the evolution of bacterial pangenomes and bacterial adaptation to new niches. However, predicting gene presence or absence can be prone to errors, which can complicate the study of HGT dynamics. This review discusses the challenges of constructing accurate pangenomes and the potential consequences of errors on downstream analyses, with the goal of improving bacterial pangenome analyses.