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Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection fo...

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Autores principales: Kalkus, Antonina, Barrett, Joy, Ashok, Theyjasvi, Morton, Brian R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8570520/
https://www.ncbi.nlm.nih.gov/pubmed/34699531
http://dx.doi.org/10.1371/journal.pcbi.1009535
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author Kalkus, Antonina
Barrett, Joy
Ashok, Theyjasvi
Morton, Brian R.
author_facet Kalkus, Antonina
Barrett, Joy
Ashok, Theyjasvi
Morton, Brian R.
author_sort Kalkus, Antonina
collection PubMed
description The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that psbA has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant psbA gene during Angiosperm evolution.
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spelling pubmed-85705202021-11-06 Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene Kalkus, Antonina Barrett, Joy Ashok, Theyjasvi Morton, Brian R. PLoS Comput Biol Research Article The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that psbA has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant psbA gene during Angiosperm evolution. Public Library of Science 2021-10-26 /pmc/articles/PMC8570520/ /pubmed/34699531 http://dx.doi.org/10.1371/journal.pcbi.1009535 Text en © 2021 Kalkus et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kalkus, Antonina
Barrett, Joy
Ashok, Theyjasvi
Morton, Brian R.
Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title_full Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title_fullStr Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title_full_unstemmed Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title_short Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene
title_sort evidence from simulation studies for selective constraints on the codon usage of the angiosperm psba gene
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8570520/
https://www.ncbi.nlm.nih.gov/pubmed/34699531
http://dx.doi.org/10.1371/journal.pcbi.1009535
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