Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 1991 Nov;129(3):873–884. doi: 10.1093/genetics/129.3.873

Molecular Analysis of the Hot Spot Region Related to Length Mutations in Wheat Chloroplast Dnas. I. Nucleotide Divergence of Genes and Intergenic Spacer Regions Located in the Hot Spot Region

Y Ogihara 1, T Terachi 1, T Sasakuma 1
PMCID: PMC1204754  PMID: 1752425

Abstract

The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.

Full Text

The Full Text of this article is available as a PDF (2.4 MB).

Selected References

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

  1. Aldrich J., Cherney B. W., Merlin E., Christopherson L. The role of insertions/deletions in the evolution of the intergenic region between psbA and trnH in the chloroplast genome. Curr Genet. 1988 Aug;14(2):137–146. doi: 10.1007/BF00569337. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Bowman C. M., Barker R. F., Dyer T. A. In wheat ctDNA, segments of ribosomal protein genes are dispersed repeats, probably conserved by nonreciprocal recombination. Curr Genet. 1988 Aug;14(2):127–136. doi: 10.1007/BF00569336. [DOI] [PubMed] [Google Scholar]
  4. Gojobori T., Li W. H., Graur D. Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol. 1982;18(5):360–369. doi: 10.1007/BF01733904. [DOI] [PubMed] [Google Scholar]
  5. Golenberg E. M., Giannasi D. E., Clegg M. T., Smiley C. J., Durbin M., Henderson D., Zurawski G. Chloroplast DNA sequence from a miocene Magnolia species. Nature. 1990 Apr 12;344(6267):656–658. doi: 10.1038/344656a0. [DOI] [PubMed] [Google Scholar]
  6. Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C. R., Meng B. Y. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet. 1989 Jun;217(2-3):185–194. doi: 10.1007/BF02464880. [DOI] [PubMed] [Google Scholar]
  7. Howe C. J., Barker R. F., Bowman C. M., Dyer T. A. Common features of three inversions in wheat chloroplast DNA. Curr Genet. 1988 Apr;13(4):343–349. doi: 10.1007/BF00424430. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci U S A. 1981 Jan;78(1):454–458. doi: 10.1073/pnas.78.1.454. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kolodner R., Tewari K. K. The molecular size and conformation of the chloroplast DNA from higher plants. Biochim Biophys Acta. 1975 Sep 1;402(3):372–390. doi: 10.1016/0005-2787(75)90273-7. [DOI] [PubMed] [Google Scholar]
  11. Li W. H., Wu C. I., Luo C. C. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol. 1984;21(1):58–71. doi: 10.1007/BF02100628. [DOI] [PubMed] [Google Scholar]
  12. Ogihara Y., Terachi T., Sasakuma T. Intramolecular recombination of chloroplast genome mediated by short direct-repeat sequences in wheat species. Proc Natl Acad Sci U S A. 1988 Nov;85(22):8573–8577. doi: 10.1073/pnas.85.22.8573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Palmer J. D., Thompson W. F. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell. 1982 Jun;29(2):537–550. doi: 10.1016/0092-8674(82)90170-2. [DOI] [PubMed] [Google Scholar]
  15. Palmer J. D., Zamir D. Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci U S A. 1982 Aug;79(16):5006–5010. doi: 10.1073/pnas.79.16.5006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Pan Z. Q., Bostock C. J. A cloning vector allowing excision of inserts with original termini irrespective of their sequence. Nucleic Acids Res. 1988 Aug 25;16(16):8182–8182. doi: 10.1093/nar/16.16.8182. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rodermel S. R., Bogorad L. Molecular evolution and nucleotide sequences of the maize plastid genes for the alpha subunit of CF1 (atpA) and the proteolipid subunit of CF0 (atpH). Genetics. 1987 May;116(1):127–139. doi: 10.1093/genetics/116.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Shinozaki K., Yamada C., Takahata N., Sugiura M. Molecular cloning and sequence analysis of the cyanobacterial gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Proc Natl Acad Sci U S A. 1983 Jul;80(13):4050–4054. doi: 10.1073/pnas.80.13.4050. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Soltis D. E., Soltis P. S., Clegg M. T., Durbin M. rbcL sequence divergence and phylogenetic relationships in Saxifragaceae sensu lato. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4640–4644. doi: 10.1073/pnas.87.12.4640. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Strauss S. H., Palmer J. D., Howe G. T., Doerksen A. H. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3898–3902. doi: 10.1073/pnas.85.11.3898. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [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]
  24. Zurawski G., Clegg M. T., Brown A. H. The Nature of Nucleotide Sequence Divergence between Barley and Maize Chloroplast DNA. Genetics. 1984 Apr;106(4):735–749. doi: 10.1093/genetics/106.4.735. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES