Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeonHalorubrum ezzemoulense

Abstract

AbstractIn this study, we use pan-genomics to characterize the organized variability from the widely dispersed halophilic archaeal speciesHalorubrum ezzemoulense. We include a multi-regional sampling of newly sequenced, high-quality draft genomes. Using the pan-genome graph of the species, we discover 50 genomic islands which represent rare accessory genetic capabilities available to members of the species. 19 of these islands are likely the remnant of mobile genetic elements and are enriched for genomic dark matter. 10 islands encode for niche adapting solute transporters, with a cosmopolitan but limited distribution throughout the strains. We also observe rearrangements which have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions (“homeocassettes”). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit extreme divergence on the amino acid level. Homeocasettes provide variations for a homologous function, which may confer a greater range of adaptability to the species group. We observe some islands that appear geographically restricted; however, we also observe the coexistence of genomes, in a single geographic region, with and without certain genomic islands, demonstrating the retention and spread of rare genes in the pangenome.