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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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Autores principales: Costantini, Maria, Cammarano, Rosalia, Bernardi, Giorgio
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
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.
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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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