PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

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Gautreau, Guillaume | Bazin, Adelme | Gachet, Mathieu | Planel, Rémi | Burlot, Laura | Dubois, Mathieu | Perrin, Amandine | Médigue, Claudine | Calteau, Alexandra | Cruveiller, Stéphane | Matias, Catherine | Ambroise, Christophe | Rocha, Eduardo, P. C. | Vallenet, David

Edité par CCSD ; PLOS -

International audience. Microorganisms have the greatest biodiversity and evolutionary history on earth. At the genomic level, it is reflected by a highly variable gene content even among organisms from the same species which explains the ability of microbes to be pathogenic or to grow in specific environments. We developed a new method called PPanGGOLiN which accurately represents the genomic diversity of a species (i.e. its pangenome) using a compact graph structure. Based on this pangenome graph, we classify genes by a statistical method according to their occurrence in the genomes. This method allowed us to build pangenomes even for uncultivated species at an unprecedented scale. We applied our method on all available genomes in databanks in order to depict the overall diversity of hundreds of species. Overall, our work enables microbiologists to explore and visualize pangenomes alike a subway map.

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