TABLE 3.

Summary of the four described hypotheses on the role and evolution of multipartite genomes^a

Hypothesis	Main tenant	Support	Contradiction(s)
Increased genome size	Dividing the genome allows for a larger genome than if only a chromosome was present	Multipartite genomes are on avg larger than nonmultipartite genomes; difference in genome sizes is due to the size of the secondary replicons and not chromosomal differences	Some small genomes are multipartite, while some large genomes are not multipartite; only 3 of the largest 50 bacterial genomes are multipartite; unclear if being multipartite allows larger genomes or if genomes are larger because they are multipartite
Increased rate of bacterial growth	Dividing the genome allows a higher growth rate due to faster replication of the genome	Some of the fastest-growing species (e.g., Vibrio) have multipartite genomes; fast-growing rhizobia contain chromids, whereas slow-growing rhizobia do not	Many slower-growing species have a multipartite genome, and some fast-growing species (e.g., Clostridium) do not have a multipartite genome; no correlation between genome size and growth rate; chromosomes and chromids are not equally sized
Coordinated gene regulation	Localization of related genes on the same replicon facilitates their coordinated regulation	The replicon that the gene is on can influence gene dosage; individual replicons are often over- or underrepresented in genes up- or downregulated in different environments	Gene dosage effect is likely limited to fast-replicating species; unclear if coordinated gene regulation was a driving force of multipartite genome evolution or a by-product of the colocalization of related genes on 1 replicon
Adaptation to novel niches	The secondary replicons are specialized for colonization and fitness in new environments	Consistent with several features of secondary replicons, including genetic variability and evolutionary rates; different replicons can show environment-specific patterns of gene regulation; secondary replicons are often enriched in genes associated with environmental adaptation	Many organisms without multipartite genomes occupy the same niches as those with multipartite genomes and display equal levels of genetic variability

^aSee Putative Advantages of Multipartite Genomes for an expanded discussion of these points.