pangenomes

A pangenome is the full complement of genes found across all strains or individuals of a species or population. It comprises a core genome, shared by all members, and an accessory genome, consisting of genes present in some but not others, including strain-specific genes. The presence-absence variation among genomes is a central feature of pangenomes.

Origin and concepts: First described for bacteria in 2005 by Tettelin et al. for Streptococcus agalactiae. Since then, pangenomes have been characterized in many bacteria, archaea, fungi, plants, and animals. A key distinction is between closed pangenomes—where most genes are shared and new genomes add few new genes—and open pangenomes, where new genomes continue to reveal many novel genes.

Data and methods: Pangenome studies assemble genomes from many isolates, cluster genes into families, and classify core vs accessory. Representations include gene presence-absence matrices and graph-based pangenomes that encode alternative paths through sequence variation. Tools like Roary, Panaroo, and PIRATE perform clustering and annotation, while graph-based frameworks such as vg or Cactus support complex structural variation.

Applications: Pangenomes improve understanding of genetic diversity and adaptation, identify virulence factors and antibiotic resistance genes, and inform crop breeding and animal health. They enable pan-genome wide association studies to link gene content with phenotypes and improve reference genomes by reducing bias.

Challenges: Large computational and data requirements, annotation inconsistencies across studies, sampling bias, and difficulties in distinguishing paralogs and horizontally transferred genes. Standardization of terminology and benchmarks is ongoing.