Challenges in prokaryote pangenomics.

Tonkin-Hill, Gerry; Corander, Jukka; Parkhill, Julian

Challenges in prokaryote pangenomics.

Authors

Tonkin-Hill, Gerry

Corander, Jukka

Parkhill, Julian

Publisher

Microbiology Society
Department of Veterinary Medicine
https://doi.org/10.1099/mgen.0.001021

Description

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.