Phylogenetic distribution of large-scale genome patchiness
<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 chromo...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-04-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/8/107 |
| _version_ | 1818321139508707328 |
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| author | Hackenberg Michael Bernaola-Galván Pedro Oliver José L Carpena Pedro |
| author_facet | Hackenberg Michael Bernaola-Galván Pedro Oliver José L Carpena Pedro |
| author_sort | Hackenberg Michael |
| collection | DOAJ |
| description | <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> |
| first_indexed | 2024-12-13T10:36:09Z |
| format | Article |
| id | doaj.art-84afd80ac2114e1dbe10a9b07f99cff3 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-13T10:36:09Z |
| publishDate | 2008-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-84afd80ac2114e1dbe10a9b07f99cff32022-12-21T23:50:43ZengBMCBMC Evolutionary Biology1471-21482008-04-018110710.1186/1471-2148-8-107Phylogenetic distribution of large-scale genome patchinessHackenberg MichaelBernaola-Galván PedroOliver José LCarpena Pedro<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>http://www.biomedcentral.com/1471-2148/8/107 |
| spellingShingle | Hackenberg Michael Bernaola-Galván Pedro Oliver José L Carpena Pedro Phylogenetic distribution of large-scale genome patchiness BMC Evolutionary Biology |
| title | Phylogenetic distribution of large-scale genome patchiness |
| title_full | Phylogenetic distribution of large-scale genome patchiness |
| title_fullStr | Phylogenetic distribution of large-scale genome patchiness |
| title_full_unstemmed | Phylogenetic distribution of large-scale genome patchiness |
| title_short | Phylogenetic distribution of large-scale genome patchiness |
| title_sort | phylogenetic distribution of large scale genome patchiness |
| url | http://www.biomedcentral.com/1471-2148/8/107 |
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