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Open Access Highly Accessed Research article

Phylogenetic distribution of large-scale genome patchiness

José L Oliver1*, Pedro Bernaola-Galván2, Michael Hackenberg13 and Pedro Carpena2

Author Affiliations

1 Dpto de Genética, Facultad de Ciencias, Universidad de Granada, Spain

2 Dpto de Física Aplicada II, Universidad de Málaga, Spain

3 Bioinformatics Group, CIC bioGUNE, CIBER-HEPAD, Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain

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BMC Evolutionary Biology 2008, 8:107  doi:10.1186/1471-2148-8-107

Published: 11 April 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.