As can be seen in Table 3, the UCEs-containing CNVs showed a lower than expected gene content, what allow us to reject this spurious association.
Indeed, obligate parasites and symbionts, which also typically present compact "genomes", can span a much wider range of genome sizes with essentially no lower limit in gene content for the extreme parasitic lifestyles of many viruses and viroids.
Of particular interest to us, we observed that the four least diverged, clonal bacterial species do not have much lower levels of variation in gene content than many of the more diverged nonclonal species (table 1).
In fungi, these "accessory" or "dispensable" chromosomes are present at different frequencies in populations and are usually characterized by higher repetitive DNA content and lower gene density when compared to the core chromosomes.
This represents a 30 39% shared content (based on the two different array sizes), which is much lower than the 78 85% shared gene content of their whole genomes when compared with the same homology criteria (BLAST cut-off of 1E-10).
Lower gene densities and higher satellite DNA content were detected in pericentromeric regions and region 1q22 in the homomorphic sex-determining chromosome 1, which also contains the ribosomal DNA locus.
Both the lower gene density and higher transposable element content in the non-recombining region of the mating-type chromosome relative to autosomal regions are consistent with a reduced efficiency of purifying selection due to the suppression of recombination, as occur on non-recombining sex chromosomes [ 59].
Therefore, lower genomic fluidity corresponds to a higher similarity in gene content.
The SNP density was around 5% lower on the microchromosomes, most likely because of their higher gene content.
Generally, mitochondrial gene content and gene order are highly conserved at the lower taxonomic rank (i.e. family and genus), but gene content variation and arrangement have reported for the genera Leptotrombidium [ 10, 13] and Dermatophagoides [ 14, 15].
