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History of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes

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dc.contributor.authorSloan, Daniel B., author
dc.contributor.authorWu, Zhiqiang, author
dc.contributor.authorOxford University Press, publisher
dc.date.accessioned2007-01-03T06:42:08Z
dc.date.available2007-01-03T06:42:08Z
dc.date.issued2014-12
dc.description.abstractAngiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.
dc.description.sponsorshipPublished with support from the Colorado State University Libraries Open Access Research and Scholarship Fund.
dc.format.mediumborn digital
dc.format.mediumarticles
dc.identifier.bibliographicCitationSloan, Daniel B. and Zhiqiang Wu, History of Plastid DNA Insertions Reveals Weak Deletion and AT Mutation Biases in Angiosperm Mitochondrial Genomes. Genome Biology and Evolution 6, issue 12 (December 2014): 3210-3221. https://dx.doi.org/10.1093/gbe/evu253
dc.identifier.doihttps://dx.doi.org/10.1093/gbe/evu253
dc.identifier.urihttp://hdl.handle.net/10217/89197
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartofOpen Access Research and Scholarship Fund (OARS)
dc.rights.licenseThis article is open access and distributed under the terms and conditions of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0/
dc.subjectindel bias
dc.subjectintracellular gene transfer
dc.subjectchloroplast
dc.subjectmutational spectrum
dc.subjectplant mitochondria
dc.titleHistory of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes
dc.typeText

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