Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination

Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. The multi-origin main chromosome has split into two genome elements via homologous recombination. The newly generated elements possess all the features of bona fide chromosomes. To our knowledge, the spontaneous generation of a new chromosome in prokaryotes without horizontal gene transfer has not been reported previously. Measurement of genome replication time in Haloferax volcanii: a replicating sample (from log phase) was obtained from H26 laboratory strain, H1689 orc5 and H2202 orc3 orc5 mutants. Replicating samples were normalyzed to a non-replicating sample of H26 laboratory strain (from stationary phase).