| Summary: | <p>Abstract</p> <p>Background</p> <p>The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequence, an evolutionary comparative analysis can be carried out at the sequence level.</p> <p>Results</p> <p>The local variations in the scaling exponent of the Detrended Fluctuation Analysis are used here to analyze large-scale genome structure and directly uncover the characteristic scales present in genome sequences. Furthermore, through shuffling experiments of selected genome regions, computationally-identified, isochore-like regions were identified as the biological source for the uncovered large-scale genome structure. The phylogenetic distribution of short- and large-scale patchiness was determined in the best-sequenced genome assemblies from eleven eukaryotic genomes: mammals (<it>Homo sapiens</it>, <it>Pan troglodytes</it>, <it>Mus musculus</it>, <it>Rattus norvegicus</it>, and <it>Canis familiaris</it>), birds (<it>Gallus gallus</it>), fishes (<it>Danio rerio</it>), invertebrates (<it>Drosophila melanogaster and Caenorhabditis elegans</it>), plants (<it>Arabidopsis thaliana</it>) and yeasts (<it>Saccharomyces cerevisiae</it>). We found large-scale patchiness of genome structure, associated with <it>in silico </it>determined, isochore-like regions, throughout this wide phylogenetic range.</p> <p>Conclusion</p> <p>Large-scale genome structure is detected by directly analyzing DNA sequences in a wide range of eukaryotic chromosome sequences, from human to yeast. In all these genomes, large-scale patchiness can be associated with the isochore-like regions, as directly detected <it>in silico </it>at the sequence level.</p>
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