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 del ta-distances) and of of olgonucleotide compositional extremes. It is s hown that delta-distances between different genomic sequences in the s ame species are low, only about 2 or 3 times the distance found in ran dom DNA, and are generally smaller than the between-species delta-dist ances. Extremes in short oligonucleotides include underrepresentation of TpA and overrepresentation of GpC in most temperate bacteriophage s equences; underrepresentation of CTAG in most eubacterial genomes; und errepresentation of GATC in most bacteriophage; CpG suppression in ver tebrates, in all animal mitochondrial genomes, and in many thermophili c bacterial sequences; and overrepresentation of GpG/CpC in ail animal mitochondrial sets and chloroplast genomes. Interpretations center on DNA structures (dinucleotide stacking energies, DNA curvature and sup erhelicity, nucleosome organization), context-dependent mutational eve nts, methylation effects, and processes of replication and repair.