Phylogenetic distribution of large-scale genome patchiness Oliver, José Luis Bernaola-Galván, Pedro Hackenberg , Michael Carpena, Pedro Animals Arabidopsis Computational biology Dogs Genome Isochores Mice Pan troglodytes Phylogeny Saccharomyces cerevisiae Sequence analysis Species specificity [Background] 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. [Results] 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 (Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, and Canis familiaris), birds (Gallus gallus), fishes (Danio rerio), invertebrates (Drosophila melanogaster and Caenorhabditis elegans), plants (Arabidopsis thaliana) and yeasts (Saccharomyces cerevisiae). We found large-scale patchiness of genome structure, associated with in silico determined, isochore-like regions, throughout this wide phylogenetic range. [Conclusion] 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 in silico at the sequence level. 2014-04-02T08:25:51Z 2014-04-02T08:25:51Z 2008 info:eu-repo/semantics/article Oliver, J.L.; Bernaola-Galván, P.; Hackenberg, M.; Carpena, P. Phylogenetic distribution of large-scale genome patchiness. BMC Evolutionary Biology, 8: 107 (2008). [http://hdl.handle.net/10481/31186] 1471-2148 doi: 10.1186/1471-2148-8-107 http://hdl.handle.net/10481/31186 eng http://creativecommons.org/licenses/by-nc-nd/3.0/ info:eu-repo/semantics/openAccess Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Biomed Central