Assembly of two Acanthamoeba castellanii strains and infection by Legionella pneumophila

A. castellanii is an amoeba host to many intracellular parasites. Neff and C3 are the most widely used strains in experimental research. Here we used a hybrid approach combining Oxford Nanopore long reads, Hi-C and shotgun to assemble and annotate the genomes of both strains. We then perform comparative genomics to investigate differences in their genomes. Finally, we infected the C3 strain with Legionella pneumophila, an intracellular bacterium and natural parasite of A. castellanii, to investigate resulting structural changes in host chromosomes following infection.