Plant mitochondrial genome evolution and structure has been shaped by double-strand break repair and recombination

Plant mitochondrial genomes are large but contain a small number of genes. These genes have very low mutation rates, but genomes rearrange and expand at significant rates. We propose that much of the apparent complexity of plant mitochondrial genomes can be explained by the interactions of double-strand break repair, recombination, and selection. One possible explanation for the disparity between the low mutation rates of genes and the high divergence of non-genes is that synonymous mutations in genes are not truly neutral. In some species, rps14 has been duplicated in the nucleus, allowing the mitochondrial copy to become a pseudogene. By measuring the synonymous substitution rate of rps14 genes and the total substitution rate of Ψrps14 pseudogenes we inferred that synonymous mutations in plant mitochondrial genes are not truly neutral. Plant mitochondrial genomes contain many repeated sequences and little is known about their evolution. We wrote a Python script that utilizes BLAST to identify and organize repeated sequences in DNA. Using this program on a large number of species from many different lineages of plants, we found that large repeats above 1kb are found only in the tracheophytes, and repeats larger than 10kb are unique to angiosperms. We proposed that the creation and maintenance of these repeats may be a side effect of the DNA repair pathways necessary to survive desiccation during seed or spore formation. To test our hypothesis that double-strand break repair is a generalized DNA repair pathway in plant mitochondria, we examined an Arabidopsis thaliana uracil DNA N-glycosylase (UNG) mutant, which cannot repair uracil in DNA through the base excision repair pathway. We set up a mutation-accumulation study, growing independent ung mutant lines for 10 generations and sequencing the mitochondrial genome with next-generation sequencing. No mutations had reached fixation in any of the sequenced lines, and the rate of heteroplasmic mutation accumulation was not different from wild-type. Using RT-PCR, we found that genes involved in double strand break repair were transcriptionally elevated. Clearly double strand break repair is an effective and generalized form of DNA repair in plant mitochondria. Adviser: Alan C. Christense