pangenomeihin

The term pangenome refers to the complete set of genes represented in all strains of a particular species or within a taxonomic group. It extends beyond a single reference genome by incorporating genetic material that is present in some members but absent in others, thereby capturing the full spectrum of genetic diversity. The concept was first formalized in 2007 by Good and colleagues, who introduced the idea while analysing genome variation in the bacterium Mycobacterium tuberculosis.

A pangenome is typically divided into a core genome, which contains genes found in every strain, and an accessory genome, which comprises genes that are variably present. The accessory component often includes mobile genetic elements, pathogenicity islands or genes that confer environmental adaptation. In some organisms the accessory portion can be substantial, reflecting processes such as horizontal gene transfer and rapid evolution.

Constructing a pangenome usually involves sequencing multiple isolates, assembling their genomes, and performing comparative analyses to identify shared and unique genes. Bioinformatics pipelines generate gene presence–absence matrices, which are analysed with clustering and phylogenetic methods to infer evolutionary relationships and reconstruct genome evolutionary histories. Advancements in long‑read sequencing and improved assembly algorithms have increased the accuracy of pangenome reconstructions, particularly for complex eukaryotic genomes.

Pangenomic studies are applied across microbiology, plant breeding, and conservation biology. In microbes they aid in understanding pathogenicity, antibiotic resistance, and ecological niche adaptation. In agricultural species, pangenomes can reveal alleles linked to yield or disease resistance that may be absent from the canonical reference, informing breeding programs. In conservation, pangenomic data help assess genetic resilience of endangered populations. The pangenome framework thus provides a comprehensive view of genetic variation, informing both basic evolutionary research and practical applications.