Chromids,[1] formerly (and less specifically) secondary chromosomes,[a] are a class of bacterial replicons (replicating DNA molecules).
Chromids also share many genomic signatures of the chromosome, including their GC-content and their codon usage bias.
Chromids also appear to be more common in bacteria which have a symbiotic or pathogenic relationship with eukaryotes[6] and with organisms with high tolerance to abiotic stressors.
The plasmid hypothesis is presently widely accepted, although there may be rare cases where large replicons originate from a chromosomal schism.
[9] The first example of this was Rhodobacter sphaeroides in 1989,[8] but additional discoveries quickly followed with Brucella melitensis in 1993,[10] Burkholderia cepacia complex in 1994,[11] Rhizobium meliloti in 1995,[12] Bacillus thuringiensis in 1996,[13] and now about 10% of bacterial species are known to have large replicons that are separate from the main chromosome.
With the onset of these discoveries, several approaches in classifying different components of multipartite genomes were proposed.
Criteria used to distinguish between these replicons typically revolve around features such as size and the presence of core genes.
This expectation existed because of the general tendency for evolutionary lineages to produce ambiguous systems, which has resulted in the more well-known issues in formulating a widely-encompassing species definition.
Members of the RLC clade have nine replicons, of which the main chromosome is the largest and the rrn-plasmid is the smallest at only 9.4kb.
This distinctive collection of features led the scientists discovering this replicon to simply classify it as an rrn-plasmid, which is thought of as a separate classification than a "plasmid" or "chromid".
It has also been observed that chromids tend to have a low copy number in the cell, as with chromosomes and megaplasmids.
[6] One of the largest chromids is the one in Burkholderia pseudomallei, which exceeds 3.1 million nucleotides in size, i.e. 3.1 megabases or 3.1 Mb.
[18] Chromids more frequently have a lower G + C content compared with the main chromosome, although the strength of this association is not very strong.
[5][19] One analysis found that chromids had a median 0.34% difference in GC content with the main chromosome, compared with values of 1.9% for megaplasmids and 2.8% for plasmids.
All chromids of a genus may additionally share a large number of conserved but non-essential genes which help define the phenotype of the genus (and the emergence of chromids appears to be the primary evolutionary force in the formation of chromid-encoding bacterial genera, as has been suggested in the case of Vibrio[19]).
In contrast, bacterial chromosomes may universally or near-universally share hundreds of conserved core genes.
[22] Due to their stable presence within a bacterial genus, chromids also have a feature of being phylogenetically restricted to specific genera.
This may result in the tendency of organisms to lose their megaplasmids over time, compared with the inherently greater evolutionary stability of chromids.
The chromid is smaller than the chromosome, and so takes a shorter amount of time to finish replication.
This is similar to F1 and P plasmids which also depend on DnaA but still have their replication controlled by other proteins (specifically RepA and RepE).
The existence of the duplicate core gene may degenerate on the main chromosome, leading to its sole presence on the newly formed chromid.
[5] Plasmids are almost always if not always the source for the origins of chromids, but at least two bacterial strains may have their large replicons derive from the schism of a larger chromosome.
In these exceptional cases, the term "secondary chromosome" may be retained to describe them and so, in this sense, differentiate them from "chromids".
It has been observed that bacteria with chromids are capable of growing faster in culture, and also contain fairly more sizable genomes.
For this reason, some have concluded that the placement of a number of genes on the chromid instead of the main chromosome allows for genome expansion without compromising replication speed and efficiency.
Instead, it is more likely that genome expansion and faster replication speed may be involved in the maintenance of chromids in lineages but not a causal explanation for their emergence.