Neo-formation of chromosomes in bacteria

The genome of bacteria is classically separated into the essential, stable and slow evolving chromosomes and the accessory, mobile and rapidly evolving plasmids. This distinction was blurred with the characterization of multipartite genomes constituted of a standard chromosome and additional essential replicons, generally thought to be adapted plasmids. Whereas chromosomes are exclusively transmitted from mother to daughter cell during the bacterial cell cycle, in general, the duplication of plasmids is unlinked to the cell cycle and their transfer to daughter cell is random. Hence, the integration of a replicon within the cell cycle is key to determining its essential nature. Here we show that the content in genes involved in the replication, partition and segregation of the replicons and in the cell cycle discriminates the bacterial replicons into chromosomes, plasmids, and another class of essential genomic elements that function as supernumerary chromosomes. These are unlikely to derive directly from plasmids. Rather, together with the chromosome, they are neochromosomes in a divided genome resulting from the fission of the fused and rearranged ancestral chromosome and plasmid. Having a divided genome appears to extend and accelerate the exploration of the genome evolutionary landscape, producing complex regulation and leading to novel eco-phenotypes and species diversification (e.g., symbionts and/or pathogens among Burkholderiales , Rhizobiales and Vibrionales).