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The sub-3 Mbp genomes from microsporidian species of the  Encephalitozoon  genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes:  Encephalitozoon intestinalis ,  Encephalitozoon cuniculi ,  Spraguea lophii ,  Trachipleistophora hominis ,  Enterocytozoon bieneusi ,  Nematocida parisii ,  Nosema bombycis  and  Nosema ceranae . While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in  S .  lophii ,  T .  hominis ,  E .  bieneusi ,  N .  parisii ,  N .  bombycis  and  N .  ceranae  are fond of A/U in third position whereas most (64.6%) optimal codons in the  Encephalitozoon  species  E .  intestinalis  and  E .  cuniculi  are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the  Encephalitozoon  genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to  Encephalitozoon  species.

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes