| Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing. | |
| | |
MedLine Citation:
|
PMID: 20424833 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
|
Since plant mitochondrial genomes exhibit some of the slowest known synonymous substitution rates, it is generally believed that they experience exceptionally low mutation rates. However, the use of synonymous substitution rates to infer mutation rates depends on the implicit assumption that synonymous sites are evolving neutrally (or nearly so). To assess the validity of this assumption in plant mitochondrial genomes, we examined coding sequence for footprints of selection acting at synonymous sites. We found that synonymous sites exhibit an AT rich and pyrimidine skewed nucleotide composition compared to both non-synonymous sites and non-coding regions. We also found some evidence for selection associated with both biased codon usage and conservation of regulatory sequences involved in mRNA processing, although some of these findings are subject to alternative non-adaptive interpretations. Regardless, the inferred strength of selection appears too weak to account for the variation in substitution rates between the mitochondrial genomes of plants and other multicellular eukaryotes. Therefore, these results are consistent with the interpretation that plant mitochondrial genomes experience a substantially lower mutation rate rather than increased functional constraints acting on synonymous sites. Nevertheless, there are important nucleotide composition patterns (particularly the differences between synonymous sites and non-coding DNA) that remain largely unexplained. |
| | |
Authors:
|
Daniel B Sloan; Douglas R Taylor |
Related Documents
:
|
19759153 - Origin and phylodynamics of rabbit hemorrhagic disease virus. 22527523 - Literature and patent analysis of the cloning and identification of human functional ge... 18944543 - Watermelon chlorotic stunt virus from the sudan and iran: sequence comparisons and iden... |
Publication Detail:
|
Type: Journal Article; Research Support, U.S. Gov't, Non-P.H.S. Date: 2010-04-28 |
Journal Detail:
|
Title: Journal of molecular evolution Volume: 70 ISSN: 1432-1432 ISO Abbreviation: J. Mol. Evol. Publication Date: 2010 May |
Date Detail:
|
Created Date: 2010-05-26 Completed Date: 2010-09-09 Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 0360051 Medline TA: J Mol Evol Country: Germany |
Other Details:
|
Languages: eng Pagination: 479-91 Citation Subset: IM |
Affiliation:
|
Department of Biology, University of Virginia, Charlottesville, VA 22904, USA. dbs4a@virginia.edu |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
Base Composition Codon* Conserved Sequence DNA Fingerprinting DNA, Mitochondrial / genetics Evolution, Molecular Genome, Mitochondrial* Genome, Plant* Plants / genetics* RNA Editing* Reproducibility of Results Selection, Genetic |
| Chemical | |
Reg. No./Substance:
|
0/Codon; 0/DNA, Mitochondrial |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: To Professor Giovanni Ruggiero.
Next Document: Changes in the intestinal microbiota of wild Atlantic cod Gadus morhua L. upon captive rearing.