Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome View Full Text


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Article Info

DATE

1995-11

AUTHORS

Brian R. Morton, Michael T. Clegg

ABSTRACT

Nucleotide sequence from a region of the chloroplast genome is presented for 12 species spanning four subfamilies of the grass family. The region contains the coding sequence for the rbcL gene and the intergenic spacer between the gene coding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the photosystem I gene psaI. This intergenic spacer contains a pseudogene for rpl23 as well as two noncoding segments with different A+T contents. Using the sequence of rbcL a chloroplast phylogeny of this family was constructed by parsimony. Variable sites of the two noncoding segments were traced onto the phylogeny to study the dynamics of base substitution. This was also performed for the fourfold-degenerate sites of the rbcL gene. A wide variation in transversion/transition is observed between the two noncoding segments and between the noncoding DNA and the fourfold-degenerate sites of rbcL. This variation is correlated with regional A+T content. As regional A+T content decreases, the ratio of transversions to transitions also decreases. Substitutions were then scored in relation to neighboring base composition. The composition of the two bases immediately flanking each substitution is highly correlated with the transversion/transition bias. When both the 5' and 3' flanking bases are an A or a T, transversions are observed 2.2 times as frequently as transitions. When either or both neighbors are a C or a G, the opposite trend is found; transitions are observed 1.5 times more frequently than transversions. More... »

PAGES

597-603

References to SciGraph publications

  • 1987-06. Drosophila mitochondrial DNA: Conserved sequences in the A+T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA in JOURNAL OF MOLECULAR EVOLUTION
  • 1991-08. Mitochondrial DNA sequence divergence in theMelanogaster and oriental species subgroups ofDrosophila in JOURNAL OF MOLECULAR EVOLUTION
  • 1976-09. Complementary base pairing and the origin of substitution mutations in NATURE
  • 1992-03. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations in JOURNAL OF MOLECULAR EVOLUTION
  • 1982-03. Biases of the estimates of DNA divergence obtained by the restriction enzyme technique in JOURNAL OF MOLECULAR EVOLUTION
  • 1993-10. A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae) in CURRENT GENETICS
  • 1982-07. Mitochondrial DNA sequences of primates: Tempo and mode of evolution in JOURNAL OF MOLECULAR EVOLUTION
  • 1984-11. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications in JOURNAL OF MOLECULAR EVOLUTION
  • 1982-09. Patterns of nucleotide substitution in pseudogenes and functional genes in JOURNAL OF MOLECULAR EVOLUTION
  • 1992-10. Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants in JOURNAL OF MOLECULAR EVOLUTION
  • 1989-06. 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 in MOLECULAR GENETICS AND GENOMICS
  • 1987-11. Tempo and mode of sequence evolution in mitochondrial DNA of HawaiianDrosophila in JOURNAL OF MOLECULAR EVOLUTION
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/bf00175818

    DOI

    http://dx.doi.org/10.1007/bf00175818

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/7490774


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