plant mitochondria

Christensen AC 2013 Plant mitochondrial genome evolution can be explained by DNA repair mechanisms. Genome Biol Evol 5:1079-1086.

  • plant mitochondrial genomes are notorious for their large and variable size, nonconserved open reading frames of unknown function, and high rates of rearrangement
  • mutation rates can only be measured in sequences that can be aligned
  • within genes, a bias toward gene conversion would keep measured mutation rates low
  • in noncoding regions, break-induced replication (BIR) explains the expansion and rearrangements
  • both processes are types of double-strand break repair
  • enhanced second-strand capture in transcribed regions versus BIR in nontranscribed regions can explain the two seemingly contradictory features of plant mitochondrial genome evolution—the low mutation rates in genes and the striking expansions of noncoding sequences
  • the low mutation rates and the expansion of the genomes have been explained by the mutational burden hypothesis
  • a few species with both highly expanded genomes and high mutation rates are a difficulty for this hypothesis
  • the divergence time between the Col-0 and C24 ecotypes of A. thaliana is approximately 0.2 Ma
  • the synonymous substitution rate in exons is either 0 or 8.4 × 10−10 per site per year
  • the mutation rate in mitochondrial noncoding regions is 9.6 × 10−10 substitutions per site per year
  • a complete mitochondrial genome sequence from A. lyrata is not currently available as an outgroup
  • comparison to the related species Raphanus sativus (AB694744) allows inference of parts of the ancestral sequence
  • alignment of the R. sativus mitochondrial genome is possible for 39 of the 103 differences between Col-0 and C24 revealing the spectrum of mutations in the Arabidopsis lineage
  • a 221,344-bp sequence ... constructed by deleting the conserved regions represents 60% of the genome and shows no similarity to GenBank entries outside the Brassicales, using MegaBLAST
  • this comparison suggests that 60% of the Arabidopsis mitochondrial genome has no function at all and could properly be called "junk"
  • the low mutation rates in plant mitochondria have been a challenge to explain
  • the low mutation rates in genes must be contrasted with the high rates of rearrangement and mutation in noncoding sequences
  • the lack of synonymous substitutions is suggestive of accurate template-directed repair
  • I suggest that gene conversion is the mechanism of repair in coding regions
  • BIR in noncoding regions and gene conversion in transcribed regions would explain both the phenomena of genome expansion and the low mutation rate in genes
  • occasional repair by error-prone processes in noncoding regions, perhaps associated with the duplications and rearrangements mediated by BIR and nonhomologous end-joining can then explain the rapid divergence of noncoding regions
  • in rare lineages there are both high mutation rates in genes and even more dramatic expansions of the genome
  • in these rare lineages, the spectrum of mutations will be biased, revealing which repair pathway is defective
  • the bias will be different in different lineages depending on which repair pathway is/was impaired