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Related Experiment Videos

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome

Tracey A Ruhlman1, Jin Zhang2, John C Blazier2

  • 1Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712 USA truhlman@austin.utexas.edu.

American Journal of Botany
|April 13, 2017
PubMed
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Recombination-dependent replication (RDR) and gene conversion between large repeats in plastid genomes (plastomes) explain structural variations, challenging previous inversion hypotheses. This mechanism shapes plastome architecture, especially in repeat-rich genomes.

Area of Science:

  • Plant genomics
  • Molecular evolution
  • Genetics

Background:

  • The orientation of single-copy regions in plastid genomes (plastomes) is often misinterpreted in scientific literature.
  • Previous hypotheses attributed single-copy inversions to intramolecular recombination between inverted repeats (IR) in a circular genome.
  • An alternative mechanism, recombination-dependent replication (RDR), is proposed to better explain these observed genomic rearrangements.

Purpose of the Study:

  • To investigate the role of recombination-dependent replication (RDR) in generating sequence arrangements within plastid genomes.
  • To characterize the repeat structure and identify alternative sequence arrangements in the plastome of *Monsonia emarginata*.
  • To challenge existing models of plastome inversion and propose a new mechanism involving RDR and gene conversion.
Keywords:
GeraniaceaeRDRchloroplastinverted repeatsplastomeptDNArecombinationreplicationunit-genome

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Main Methods:

  • Utilized Illumina paired-end and PacBio single-molecule real-time (SMRT) sequencing for repeat structure characterization.
  • Employed OrgConv and nucleotide alignments to infer ancestral nucleotides and identify gene conversion events among repeats.
  • Mapped long SMRT reads to the *M. emarginata* unit-genome assembly to detect alternative sequence arrangements.

Main Results:

  • Identified large repeats (>1 kilobase) constituting approximately 22% of the *M. emarginata* plastome.
  • Observed GC-biased gene conversion among repeats larger than 2 kilobases.
  • Detected alternative, substoichiometric sequence arrangements through mapping of long SMRT reads.

Conclusions:

  • Proposed a model where RDR and gene conversion between long repeats drive variations in plastome unit-genome structure.
  • Provided evidence supporting both intra- and intermolecular recombination between large repeats as key drivers of structural diversity.
  • Concluded that these mechanisms homogenize repeat sequences while varying overall plastome structure, particularly in repeat-rich genomes.