Warren, Jessica M., authorSimmons, Mark P., authorWu, Zhiqiang, authorSloan, Daniel B., authorOxford University Press, publisher2016-05-042016-05-042016Warren, Jessica M., Mark P. Simmons, Zhiqiang Wu, and Daniel B. Sloan, Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes. Genome Biology and Evolution 8, no. 2 (February 2016): 364-374. http://dx.doi.org/10.1093/gbe/evw003http://hdl.handle.net/10217/172747The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.born digitalarticlesengangiospermsDNA polymerasemitochondrial plasmidsmutation ratemtDNATextThis 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).https://dx.doi.org/10.1093/gbe/evw003