title: Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera.
abstract: Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Amid
authors.initials: A
authors.lastname: Massouh
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Schubert
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Liliya
authors.initials: L
authors.lastname: Yaneva-Roder
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Elena S
authors.initials: ES
authors.lastname: Ulbricht-Jones
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Arkadiusz
authors.identifier: 0000-0002-8633-6044
authors.initials: A
authors.lastname: Zupok
authors.affiliation: Department of Biology, University of Toronto-Mississauga, Mississauga, Ontario L5L 1C6, Canada.
authors.forename: Marc T J
authors.initials: MT
authors.lastname: Johnson
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
authors.forename: Stephen I
authors.initials: SI
authors.lastname: Wright
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Tommaso
authors.initials: T
authors.lastname: Pellizzer
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Johanna
authors.initials: J
authors.lastname: Sobanski
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany.
authors.forename: Ralph
authors.identifier: 0000-0001-7502-6940
authors.initials: R
authors.lastname: Bock
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany greiner@mpimp-golm.mpg.de.
authors.forename: Stephan
authors.initials: S
authors.lastname: Greiner
mesh_terms: D002736:Chloroplasts / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics / Q000502:physiology; D018744:DNA, Plant / Q000235:genetics; D009154:Mutation / Q000235:genetics; D031664:Oenothera / Q000235:genetics*; D018087:Plastids / Q000235:genetics
chemical_list: D018744:DNA, Plant