Journal
MOLECULAR PHYLOGENETICS AND EVOLUTION
Volume 65, Issue 1, Pages 339-344Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2012.06.017
Keywords
Genome architecture; Mitochondrial DNA; Mutation rate; Plastid DNA; Substitution rate
Funding
- National Science Foundation (NSF) [0741907, EF-0626678, 0732440]
- National Oceanic and Atmospheric Administration (NOAA) [NA06OAR4170108, R/A-38]
- DOE JGI [DE-AC02-05CH11231]
- Division of Environmental Biology [1004213]
- Natural Sciences and Engineering Research Council of Canada (NSERC)
- NSERC [227301]
- Izaak Walton Killam Trusts
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [0741907] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [0732440] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [1004213] Funding Source: National Science Foundation
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In photosynthetic eukaryotes, relative silent-site nucleotide substitution rates (which can be used to approximate relative mutation rates) among mitochondrial, plastid, and nuclear genomes (mtDNAs, ptDNAs, and nucDNAs) are estimated to be 1:3:10 respectively for seed plants and roughly equal for green algae. These estimates correlate with certain genome characteristics, such as size and coding density, and have therefore been taken to support a relationship between mutation rate and genome architecture. Plants and green algae, however, represent a small fraction of the major eukaryotic plastid-bearing lineages. Here, we investigate relative rates of mutation within the model red algal genus Porphyra. in contrast to plants, we find that the levels of silent-site divergence between the Porphyra purpurea and Porphyra umbilicalis mtDNAs are three times that of their ptDNAs and five times that of their nucDNAs. Moreover, relative mutation rates do not correlate with genome architecture: despite an estimated threefold difference in their mutation rate, the mitochondrial and plastid genome coding densities are equivalent - an observation that extends to organisms with secondary red algal plastids. These findings are supported by within-species silent-site polymorphism data from P. purpurea. (C) 2012 Elsevier Inc. All rights reserved.
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