COMPOSITIONAL DIFFERENCES WITHIN AND BETWEEN EUKARYOTIC GENOMES

Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Compa risons within and between species sample sequences are based on the pr ofile of dinucleotide relative abundance values (The profile is rho(XY ) = f(XY)*/f(X)*f(Y)* for all XY, where f(X)* denotes the frequency o f the nucleotide X and f(XY) denotes the frequency of the dinucleotid e XY, both computed from the sequence concatenated with its inverted c omplement), Previous studies with respect to prokaryotes and this stud y document that profiles of different DNA sequence samples (sample siz e greater than or equal to 50 kb) from the same organism are generally much more similar to each other than they are to profiles from other organisms, and that closely related organisms generally have more simi lar profiles than do distantly related organisms, On this basis we ref er to the collection {rho(XY)} as the genome signature. This paper id entifies rho(XY) extremes and compares genome signature differences f or a diverse range of eukaryotic species. Interpretations on the mecha nisms maintaining these profile differences center on genome-wide repl ication, repair, DNA structures, and context-dependent mutational bias es, It is also observed that mitochondrial genome signature difference s between species parallel the corresponding nuclear genome signature differences despite large differences between corresponding mitochondr ial and nuclear signatures. The genome signature differences also have implications for contrasts between rodents and other mammals, and bet ween monocot and dicot plants, as well as providing evidence for simil arities among fungi and the diversity of protists.