publication . Article . 2014

A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.

Elhaik, E.; Graur, D.;
Open Access English
  • Published: 06 Nov 2014 Journal: PLoS Computational Biology, volume 10, issue 11 (issn: 1553-734X, eissn: 1553-7358, Copyright policy)
  • Publisher: Public Library of Science
  • Country: United Kingdom
Abstract
Author Summary The non-uniformity of DNA composition in mammalian genomes has been known for over four decades. Many attempts have been made to provide a concise description of this heterogeneity and to identify the evolutionary driving forces behind this compositional phenomenology. The first concise description of the genome suggested an isochoric structure according to which the mammalian genome consists of a mosaic of long, compositionally homogenous DNA sequences. With the advent of genome sequencing, this description was found to be inappropriate. We have recently proposed an alternative “compositional domains” model that depicts the human and cow genomes ...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Computational Biology, Evolutionary Modeling, Genome Evolution, Genomics Statistics, Evolutionary Biology, Evolutionary Theory, Molecular Evolution, Biology (General), QH301-705.5, Ecology, Modelling and Simulation, Computational Theory and Mathematics, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Cellular and Molecular Neuroscience, Clade, Phylogenetics, Genome, Genomics, GC-content, Bioinformatics, Euarchontoglires, biology.organism_classification, biology, Phylogenetic tree, Domain model
76 references, page 1 of 6

1. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.

2. Elhaik E, Graur D, Josic´ K (2010) Comparative testing of DNA segmentation algorithms using benchmark simulations. Mol Biol Evol 27: 1015-1024.

3. Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108: 237-254.

4. Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108: 219-235.

5. Cuny G, Soriano P, Macaya G, Bernardi G (1981) The major components of the mouse and human genomes: Preparation, basic properties and compositional heterogeneity. Eur J Biochem 115: 227-233.

6. Bernardi G, Bernardi G (1985) Codon usage and genome composition. J Mol Evol 22: 363-365. [OpenAIRE]

7. Li W, Bernaola-Galva´n P, Carpena P, Oliver JL (2003) Isochores merit the prefix 'iso'. Comput Biol Chem 27: 5-10.

8. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, et al. (1985) The mosaic genome of warm-blooded vertebrates. Science 228: 953-958. [OpenAIRE]

9. Bernardi G (2001) Misunderstandings about isochores. Part 1. Gene 276: 3-13.

10. Clay O, Carels N, Douady C, Macaya G, Bernardi G (2001) Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses. Gene 276: 15-24.

11. Oliver JL, Carpena P, Roma´n-Rolda´n R, Mata-Balaguer T, Mejia´s-Romero A, et al. (2002) Isochore chromosome maps of the human genome. Gene 300: 117- 127. [OpenAIRE]

12. Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241: 3-17.

13. Pavlicek A, Paces J, Clay O, Bernardi G (2002) A compact view of isochores in the draft human genome sequence. FEBS Lett 511: 165-169. [OpenAIRE]

14. Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar JV, et al. (2001) Similar integration but different stability of Alus and LINEs in the human genome. Gene 276: 39-45. [OpenAIRE]

15. Elhaik E, Graur D, Josic K, Landan G (2010) Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm. Nucleic Acids Res 38: e158. [OpenAIRE]

76 references, page 1 of 6
Abstract
Author Summary The non-uniformity of DNA composition in mammalian genomes has been known for over four decades. Many attempts have been made to provide a concise description of this heterogeneity and to identify the evolutionary driving forces behind this compositional phenomenology. The first concise description of the genome suggested an isochoric structure according to which the mammalian genome consists of a mosaic of long, compositionally homogenous DNA sequences. With the advent of genome sequencing, this description was found to be inappropriate. We have recently proposed an alternative “compositional domains” model that depicts the human and cow genomes ...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Computational Biology, Evolutionary Modeling, Genome Evolution, Genomics Statistics, Evolutionary Biology, Evolutionary Theory, Molecular Evolution, Biology (General), QH301-705.5, Ecology, Modelling and Simulation, Computational Theory and Mathematics, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Cellular and Molecular Neuroscience, Clade, Phylogenetics, Genome, Genomics, GC-content, Bioinformatics, Euarchontoglires, biology.organism_classification, biology, Phylogenetic tree, Domain model
76 references, page 1 of 6

1. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.

2. Elhaik E, Graur D, Josic´ K (2010) Comparative testing of DNA segmentation algorithms using benchmark simulations. Mol Biol Evol 27: 1015-1024.

3. Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108: 237-254.

4. Thiery JP, Macaya G, Bernardi G (1976) An analysis of eukaryotic genomes by density gradient centrifugation. J Mol Biol 108: 219-235.

5. Cuny G, Soriano P, Macaya G, Bernardi G (1981) The major components of the mouse and human genomes: Preparation, basic properties and compositional heterogeneity. Eur J Biochem 115: 227-233.

6. Bernardi G, Bernardi G (1985) Codon usage and genome composition. J Mol Evol 22: 363-365. [OpenAIRE]

7. Li W, Bernaola-Galva´n P, Carpena P, Oliver JL (2003) Isochores merit the prefix 'iso'. Comput Biol Chem 27: 5-10.

8. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, et al. (1985) The mosaic genome of warm-blooded vertebrates. Science 228: 953-958. [OpenAIRE]

9. Bernardi G (2001) Misunderstandings about isochores. Part 1. Gene 276: 3-13.

10. Clay O, Carels N, Douady C, Macaya G, Bernardi G (2001) Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses. Gene 276: 15-24.

11. Oliver JL, Carpena P, Roma´n-Rolda´n R, Mata-Balaguer T, Mejia´s-Romero A, et al. (2002) Isochore chromosome maps of the human genome. Gene 300: 117- 127. [OpenAIRE]

12. Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241: 3-17.

13. Pavlicek A, Paces J, Clay O, Bernardi G (2002) A compact view of isochores in the draft human genome sequence. FEBS Lett 511: 165-169. [OpenAIRE]

14. Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar JV, et al. (2001) Similar integration but different stability of Alus and LINEs in the human genome. Gene 276: 39-45. [OpenAIRE]

15. Elhaik E, Graur D, Josic K, Landan G (2010) Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm. Nucleic Acids Res 38: e158. [OpenAIRE]

76 references, page 1 of 6
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