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Phylogenetic distribution of large-scale genome patchiness
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 computationa...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397391/ https://www.ncbi.nlm.nih.gov/pubmed/18405379 http://dx.doi.org/10.1186/1471-2148-8-107 |
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author | Oliver, José L Bernaola-Galván, Pedro Hackenberg, Michael Carpena, Pedro |
author_facet | Oliver, José L Bernaola-Galván, Pedro Hackenberg, Michael Carpena, Pedro |
author_sort | Oliver, José L |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2397391 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-23973912008-05-29 Phylogenetic distribution of large-scale genome patchiness Oliver, José L Bernaola-Galván, Pedro Hackenberg, Michael Carpena, Pedro BMC Evol Biol Research Article 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. BioMed Central 2008-04-11 /pmc/articles/PMC2397391/ /pubmed/18405379 http://dx.doi.org/10.1186/1471-2148-8-107 Text en Copyright ©2008 Oliver et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Oliver, José L Bernaola-Galván, Pedro Hackenberg, Michael Carpena, Pedro Phylogenetic distribution of large-scale genome patchiness |
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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397391/ https://www.ncbi.nlm.nih.gov/pubmed/18405379 http://dx.doi.org/10.1186/1471-2148-8-107 |
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