Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost

@article{Palmer1982ChloroplastDR,
  title={Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost},
  author={Jeffrey D. Palmer and William F. Thompson},
  journal={Cell},
  year={1982},
  volume={29},
  pages={537-550}
}
Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements
TLDR
It is concluded that the inverted repeat has been lost only once among legumes and that this loss occurred prior to all the other rearrangements observed in subclover, broad bean and pea.
Dispersed repeats and structural reorganization in subclover chloroplast DNA.
TLDR
Gene mapping of subclover chloroplast DNA reveals major structural reorganization of the genome, and a dispersed family of repeats, with each element about 1 kb in length, is present in at least six copies, which may be the first family of transposable elements found in any organelle genome.
Evolutionary significance of inversions in legume chloroplast DNAs
TLDR
Analysis of gene locations in pea cpDNA, which lacks the large inverted repeat, combined with cross-hybridization studies using 59 clones covering the mung bean genome, leads to a refined picture of the position and nature of the numerous rearrangements previously described in the pea genome.
Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda
TLDR
Each of the three fern chloroplast genomes exists as an equimolar population of two isomeric circles differing only in the relative orientation of their two single copy regions, inferred to result from high frequency intramolecular recombination between paired inverted repeat segments.
Chloroplast DNA exists in two orientations
TLDR
It is shown that chloroplast DNA prepared from a single plant of common bean (Phaseolus vulgaris) consists of two equimolar populations of molecules differing only in the relative orientation of their single copy sequences.
Structure and sequence evolution of three legume chloroplast DNAs
TLDR
Chloroplast DNAs from soybean, common bean and mung bean have been compared in overall structure and nucleotide sequence homologies and it is shown that chloroplast ribosomal DNA is relatively conserved and the two deletion/addition regions relatively diverged in base sequence.
Dispersed repetitive sequences in the chloroplast genome of Douglas-fir
TLDR
Restriction mapping and DNA sequencing were used to characterize dispersed repetitive DNA in the chloroplast genome of Douglas-fir and indicated the presence of a 633 by inverted repeat which contains a complete tRNA-Serine (GCU) gene and a highly conserved open reading frame (ORF 3.6).
Conservation of chloroplast genome structure among vascular plants
TLDR
The first physical map of a gymnosperm chloroplast genome is constructed and its organization with those of a fern and several angiosperms by heterologous filter hybridization reveals a virtually colinear arrangement of homologous sequence elements in these genomes representing three divisions of vascular plants that diverged some 200–400 million years ago.
Points of rearrangements between plastid chromosomes: location of protein coding regions on broad bean chloroplast DNA
TLDR
A model for chloroplast DNA divergence is suggested assuming that short repeats exist which are the substrate for a recombination system and that the DNAs contain short repeat sequences at some conserved positions.
Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion
TLDR
The results suggest that expansion of the inverted repeats in buckwheat chloroplast DNA might have been associated with an inversion.
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References

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Rearrangements in the chloroplast genomes of mung bean and pea.
  • J. Palmer, W. F. Thompson
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1981
We have mapped all the cleavage sites for the restriction endonucleases BstEII, Kpn I, Pst I, Pvu II, Sac I, Sal I, Sma I, and Xho I on the circular chloroplast chromosomes from mung bean and pea.
Physical and gene mapping of chloroplast DNA from Atriplex triangularis and Cucumis sativa.
TLDR
A rapid and simple method for constructing restriction maps of large DNAs (100-200 kb) is presented and the physical and genetic organization of these DNAs is compared to that of spinach chloroplast DNA.
Inverted repeats in chloroplast DNA from higher plants.
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  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1979
TLDR
It is proposed that the head-to-head circular dimers are formed by a recombination event between two circular monomers in the inverted sequence.
Chloroplast DNA Sequence Homologies among Vascular Plants.
TLDR
Determinations were made of the percentage of chloroplast DNA in total DNA extracts from different higher plants; this value remained relatively constant when compared with the large variation in the diploid genome size of the plants.
Conservation of sequence arrangement among higher plant chloroplast DNAs: molecular cross hybridization among the Solanaceae and between Nicotiana and Spinacia.
TLDR
Isolated, nick-translated Pvu II fragments of Nicotiana tabacum chloroplast DNA produce specific intra- and intergeneric hybridization signals with chloropleft DNA digests from several representatives of the Solanaceae, which permit construction of physical maps for NicOTiana line 92, Atropa belladonna and Petunia parodii.
Sequence Homology between Chloroplast DNAs from Several Higher Plants.
TLDR
The data suggest that considerable sequence homology exists between the ctDNAs of these plants and that some sequences are held in common among all of the species tested.
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