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Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

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 m...

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Autores principales: Xiang, Heng, Zhang, Ruizhi, Butler, Robert R., Liu, Tie, Zhang, Li, Pombert, Jean-François, Zhou, Zeyang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461291/
https://www.ncbi.nlm.nih.gov/pubmed/26057384
http://dx.doi.org/10.1371/journal.pone.0129223
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author Xiang, Heng
Zhang, Ruizhi
Butler, Robert R.
Liu, Tie
Zhang, Li
Pombert, Jean-François
Zhou, Zeyang
author_facet Xiang, Heng
Zhang, Ruizhi
Butler, Robert R.
Liu, Tie
Zhang, Li
Pombert, Jean-François
Zhou, Zeyang
author_sort Xiang, Heng
collection PubMed
description 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.
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spelling pubmed-44612912015-06-16 Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes Xiang, Heng Zhang, Ruizhi Butler, Robert R. Liu, Tie Zhang, Li Pombert, Jean-François Zhou, Zeyang PLoS One Research Article 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. Public Library of Science 2015-06-09 /pmc/articles/PMC4461291/ /pubmed/26057384 http://dx.doi.org/10.1371/journal.pone.0129223 Text en © 2015 Xiang et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Xiang, Heng
Zhang, Ruizhi
Butler, Robert R.
Liu, Tie
Zhang, Li
Pombert, Jean-François
Zhou, Zeyang
Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title_full Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title_fullStr Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title_full_unstemmed Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title_short Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes
title_sort comparative analysis of codon usage bias patterns in microsporidian genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461291/
https://www.ncbi.nlm.nih.gov/pubmed/26057384
http://dx.doi.org/10.1371/journal.pone.0129223
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