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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/31186

Title: Phylogenetic distribution of large-scale genome patchiness
Authors: Oliver, José Luis
Bernaola-Galván, Pedro
Hackenberg, Michael
Carpena, Pedro
Issue Date: 2008
Abstract: [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.
Sponsorship: This work was supported by the Spanish Government (BIO2005-09116-C03-01) and Plan Andaluz de Investigación (CVI-162, P06-FQM-01858, P07-FQM-03163 and TIC-640).
Publisher: Biomed Central
Keywords: Animals
Arabidopsis
Computational biology
Dogs
Genome
Isochores
Mice
Pan troglodytes
Phylogeny
Saccharomyces cerevisiae
Sequence analysis
Species specificity
URI: http://hdl.handle.net/10481/31186
ISSN: 1471-2148
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Citation: 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]
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