title: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.
abstract: OBJECTIVE
  There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements.
  
  
  METHODS
  We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome ofMonsonia emarginata(Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements.
  
  
  RESULTS
  AlthoughM. emarginatalacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to theM. emarginataunit-genome assembly revealed alternative, substoichiometric sequence arrangements.
  
  
  CONCLUSIONS
  We offer a model based on RDR and gene conversion between long repeated sequences in theM. emarginataplastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA truhlman@austin.utexas.edu.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA.
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Blazier
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JSM
authors.lastname: Sabir
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA.|Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589 Saudi Arabia.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
mesh_terms: D004261:DNA Replication / Q000235:genetics; D005785:Gene Conversion / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D054627:Genome, Plastid / Q000235:genetics*; D031314:Geraniaceae / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment
keywords: Geraniaceae; RDR; chloroplast; inverted repeats; plastome; ptDNA; recombination; replication; unit-genome