Heterogeneity of Genomes: Measures and Values

Genomic homogeneity is investigated for a broad base of DNA sequences in terms of dinucleotide relative abundance distances (abbreviated δ-distances) and of oligonucleotide compositional extremes. It is shown that δ-distances between different genomic sequences in the same species are low, only abou...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 1994-12, Vol.91 (26), p.12837-12841
Main Authors: Karlin, S., Ladunga, I., Blaisdell, B. E.
Format: Article
Language:English
Subjects:
Animals
Bacillus subtilis
Bacteria
Bacteriophages
Base Composition
Caenorhabditis elegans
Chromosomes
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA, Bacterial - chemistry
DNA, Fungal - chemistry
Eukaryotic Cells
Evolution
Genomes
Genomics
Nucleic Acid Conformation
Nucleotide sequences
Oligodeoxyribonucleotides - chemistry
Oligonucleotides
Saccharomyces cerevisiae
Sequence Analysis, DNA - methods
Species
Vertebrates
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Summary:Genomic homogeneity is investigated for a broad base of DNA sequences in terms of dinucleotide relative abundance distances (abbreviated δ-distances) and of oligonucleotide compositional extremes. It is shown that δ-distances between different genomic sequences in the same species are low, only about 2 or 3 times the distance found in random DNA, and are generally smaller than the between-species δ-distances. Extremes in short oligonucleotides include underrepresentation of TpA and overrepresentation of GpC in most temperate bacteriophage sequences; underrepresentation of CTAG in most eubacterial genomes; underrepresentation of GATC in most bacteriophage; CpG suppression in vertebrates, in all animal mitochondrial genomes, and in many thermophilic bacterial sequences; and overrepresentation of GpG/CpC in all animal mitochondrial sets and chloroplast genomes. Interpretations center on DNA structures (dinucleotide stacking energies, DNA curvature and superhelicity, nucleosome organization), context-dependent mutational events, methylation effects, and processes of replication and repair.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.91.26.12837