title: Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes.
abstract: 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.
authors.affiliation: College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
authors.forename: Heng
authors.initials: H
authors.lastname: Xiang
authors.affiliation: Biotechnology Research Center, Southwest University, Chongqing 400715, China.
authors.forename: Ruizhi
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Butler
authors.affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
authors.forename: Tie
authors.initials: T
authors.lastname: Liu
authors.affiliation: Department of Math and Information, China West Normal University, Nanchong, Sichuan 637000, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Pombert
authors.affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
authors.forename: Zeyang
authors.initials: Z
authors.lastname: Zhou
mesh_terms: D003062:Codon / Q000235:genetics*; D016819:Encephalitozoon / Q000235:genetics*; D019143:Evolution, Molecular; D016681:Genome, Fungal / Q000235:genetics*; D058507:Host Specificity / Q000235:genetics; D016814:Microsporidia / Q000235:genetics*; D009154:Mutation / Q000235:genetics
chemical_list: D003062:Codon