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. 1988 Nov;85(22):8573–8577. doi: 10.1073/pnas.85.22.8573

Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species.

Y Ogihara 1, T Terachi 1, T Sasakuma 1
PMCID: PMC282501  PMID: 3186748

Abstract

Structural alterations of the chloroplast genome tend to occur at "hot spots" on the physical map. To clarify the mechanism of mutation of chloroplast genome structure in higher plants, we determined the nucleotide sequence of the hot-spot region of chloroplast DNAs related to length mutations (deletions/insertions) in Triticum (wheat) and Aegilops. From a comparison of this region in wheat with the corresponding region of tobacco or liverwort, it is evident that one of the open reading frames in tobacco (ORF512) has been replaced in wheat by the rpl23 gene, which is a member of the ribosomal protein gene operon. In the deleted positions and in the original genome of Triticum and Aegilops, consensus sequences forming short direct repeats were found, indicating that these deletions were a result of intramolecular recombination mediated by these short direct-repeat sequences. By two independent recombination events in the Aegilops crassa type of chloroplast genome, which is shared by Triticum monococcum, Ae. bicornis, Ae. sharonensis, Ae. comosa, and Ae. mutica, the novel chloroplast DNA sequences of T. aestivum and Ae. squarrosa were generated. This finding indicates the existence of illegitimate recombination in the chloroplast genome and presents a mechanism for producing genetic diversity of that genome.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brown W. M., George M., Jr, Wilson A. C. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1967–1971. doi: 10.1073/pnas.76.4.1967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Day A., Ellis T. H. Chloroplast DNA deletions associated with wheat plants regenerated from pollen: possible basis for maternal inheritance of chloroplasts. Cell. 1984 Dec;39(2 Pt 1):359–368. doi: 10.1016/0092-8674(84)90014-x. [DOI] [PubMed] [Google Scholar]
  4. DeSalle R., Giddings L. V., Templeton A. R. Mitochondrial DNA variability in natural populations of Hawaiian Drosophila. I. Methods and levels of variability in D. silvestris and D. heteroneura populations. Heredity (Edinb) 1986 Feb;56(Pt 1):75–85. doi: 10.1038/hdy.1986.11. [DOI] [PubMed] [Google Scholar]
  5. Doebley J. F., Ma D. P., Renfroe W. T. Insertion/deletion mutations in the Zea chloroplast genome. Curr Genet. 1987;11(8):617–624. doi: 10.1007/BF00393925. [DOI] [PubMed] [Google Scholar]
  6. Döring H. P., Starlinger P. Molecular genetics of transposable elements in plants. Annu Rev Genet. 1986;20:175–200. doi: 10.1146/annurev.ge.20.120186.001135. [DOI] [PubMed] [Google Scholar]
  7. Fujimoto S., Yamagishi H. Isolation of an excision product of T-cell receptor alpha-chain gene rearrangements. Nature. 1987 May 21;327(6119):242–243. doi: 10.1038/327242a0. [DOI] [PubMed] [Google Scholar]
  8. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  9. Howe C. J. The endpoints of an inversion in wheat chloroplast DNA are associated with short repeated sequences containing homology to att-lambda. Curr Genet. 1985;10(2):139–145. doi: 10.1007/BF00636479. [DOI] [PubMed] [Google Scholar]
  10. Koller B., Fromm H., Galun E., Edelman M. Evidence for in vivo trans splicing of pre-mRNAs in tobacco chloroplasts. Cell. 1987 Jan 16;48(1):111–119. doi: 10.1016/0092-8674(87)90361-8. [DOI] [PubMed] [Google Scholar]
  11. Lonsdale D. M., Hodge T. P., Fauron C. M. The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucleic Acids Res. 1984 Dec 21;12(24):9249–9261. doi: 10.1093/nar/12.24.9249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. McLeod M., Volkert F., Broach J. Components of the site-specific recombination system encoded by the yeast plasmid 2-micron circle. Cold Spring Harb Symp Quant Biol. 1984;49:779–787. doi: 10.1101/sqb.1984.049.01.088. [DOI] [PubMed] [Google Scholar]
  13. Mickel S., Ohtsubo E., Bauer W. Heteroduplex mapping of small plasmids derived from R-factor R12: in vivo recombination occurs at IS1 insertion sequences. Gene. 1977;2(3-4):193–210. doi: 10.1016/0378-1119(77)90017-8. [DOI] [PubMed] [Google Scholar]
  14. Nicholls R. D., Fischel-Ghodsian N., Higgs D. R. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. doi: 10.1016/0092-8674(87)90289-3. [DOI] [PubMed] [Google Scholar]
  15. Ohtsubo H., Ohtsubo E. Nucleotide sequence of an insertion element, IS1. Proc Natl Acad Sci U S A. 1978 Feb;75(2):615–619. doi: 10.1073/pnas.75.2.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Okazaki K., Davis D. D., Sakano H. T cell receptor beta gene sequences in the circular DNA of thymocyte nuclei: direct evidence for intramolecular DNA deletion in V-D-J joining. Cell. 1987 May 22;49(4):477–485. doi: 10.1016/0092-8674(87)90450-8. [DOI] [PubMed] [Google Scholar]
  17. Palmer J. D. Comparative organization of chloroplast genomes. Annu Rev Genet. 1985;19:325–354. doi: 10.1146/annurev.ge.19.120185.001545. [DOI] [PubMed] [Google Scholar]
  18. Palmer J. D., Jorgensen R. A., Thompson W. F. Chloroplast DNA variation and evolution in pisum: patterns of change and phylogenetic analysis. Genetics. 1985 Jan;109(1):195–213. doi: 10.1093/genetics/109.1.195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986 Sep;5(9):2043–2049. doi: 10.1002/j.1460-2075.1986.tb04464.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Stern D. B., Gruissem W. Control of plastid gene expression: 3' inverted repeats act as mRNA processing and stabilizing elements, but do not terminate transcription. Cell. 1987 Dec 24;51(6):1145–1157. doi: 10.1016/0092-8674(87)90600-3. [DOI] [PubMed] [Google Scholar]
  22. Takeishi K., Gotoh O. Computer analysis of the sequence relationships among 4.5S RNA molecular species from various sources. J Biochem. 1982 Oct;92(4):1173–1177. doi: 10.1093/oxfordjournals.jbchem.a134033. [DOI] [PubMed] [Google Scholar]
  23. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]

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