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The evolution of isochore patterns in vertebrate genomes
BACKGROUND: Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different G...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678159/ https://www.ncbi.nlm.nih.gov/pubmed/19344507 http://dx.doi.org/10.1186/1471-2164-10-146 |
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author | Costantini, Maria Cammarano, Rosalia Bernardi, Giorgio |
author_facet | Costantini, Maria Cammarano, Rosalia Bernardi, Giorgio |
author_sort | Costantini, Maria |
collection | PubMed |
description | BACKGROUND: Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination. RESULTS: The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates. CONCLUSION: On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection. |
format | Text |
id | pubmed-2678159 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26781592009-05-07 The evolution of isochore patterns in vertebrate genomes Costantini, Maria Cammarano, Rosalia Bernardi, Giorgio BMC Genomics Research Article BACKGROUND: Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination. RESULTS: The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates. CONCLUSION: On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection. BioMed Central 2009-04-03 /pmc/articles/PMC2678159/ /pubmed/19344507 http://dx.doi.org/10.1186/1471-2164-10-146 Text en Copyright © 2009 Costantini 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 Costantini, Maria Cammarano, Rosalia Bernardi, Giorgio The evolution of isochore patterns in vertebrate genomes |
title | The evolution of isochore patterns in vertebrate genomes |
title_full | The evolution of isochore patterns in vertebrate genomes |
title_fullStr | The evolution of isochore patterns in vertebrate genomes |
title_full_unstemmed | The evolution of isochore patterns in vertebrate genomes |
title_short | The evolution of isochore patterns in vertebrate genomes |
title_sort | evolution of isochore patterns in vertebrate genomes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678159/ https://www.ncbi.nlm.nih.gov/pubmed/19344507 http://dx.doi.org/10.1186/1471-2164-10-146 |
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