Structural and evolutionary genomics : natural selection in genome evolution / Giorgio Bernardi.

Format:

Book

Author/Creator:

Bernardi, Giorgio.

Series:

New comprehensive biochemistry ; v. 37.

New comprehensive biochemistry ; v. 37

Language:

English

Subjects (All):

Genomics.

Evolutionary genetics.

Gene mapping.

Genetics.

Chromosome Mapping.

Medical Subjects:

Genomics.

Genetics.

Chromosome Mapping.

Physical Description:

xv, 434 pages : illustrations (some color) ; 25 cm.

Place of Publication:

Amsterdam ; New York : Elsevier, 2004.

Contents:

1.1 The genome: a short history of different views 3

1.2 Population genetics and molecular evolution 4

1.4 A brief chronology of our investigations 5

1.5 Molecular approaches to the study of the genome 10

Part 2 Lessons from a Small Dispensable Genome, the Mitochondrial Genome of Yeast 19

Chapter 1. The mitochondrial genome of yeast and the petite mutation 21

1.1 The "petite colonie" mutation 21

1.2 The petite mutation is accompanied by gross alterations of mitochondrial DNA 23

1.3 The AT spacers and the deletion hypothesis 23

1.4 The petite mutation is due to large deletions 25

1.5 The GC clusters 26

1.6 The excision sites 26

1.7 Genomes without genes 28

Chapter 2. The origins of replication 31

2.1 Excision and recombination 31

2.2 The canonical and the surrogate origins of replication of petite genomes 32

2.3 The replication of petite genomes and the phenomenon of suppressivity 35

2.4 The ori sequences as transcription initiation sites 37

2.5 The effect of flanking sequences on the efficiency of replication of petite genomes 38

2.6 The ori[superscript -] petites 14 and 26 39

2.7 Temperature and the replicative ability of ori[superscript -] petites 14 and 26 42

Chapter 3. The organization and evolution of the mitochondrial genome of yeast 43

3.1 The organization of the mitochondrial genome of yeast 43

3.2 The evolutionary origin of ori sequences 44

3.3 The evolutionary origin of the GC clusters 45

3.4 The evolutionary origin of the AT spacers and the var 1 gene 45

3.5 The non-coding sequences: evolutionary origin and biological role 46

Part 3 The Organization of the Vertebrate Genome 49

Chapter 1. Isochores and isochore families 51

1.1 The fractionation of the bovine genome 51

1.2 The fractionation of eukaryotic main-band DNAs 53

1.3 Isochores and isochore families 56

1.4 Isochores and the draft human genome sequence 63

1.5 Other misunderstandings about isochores 71

Chapter 2. Compositional patterns of coding sequences 75

Chapter 3. Compositional correlations between coding and non-coding sequences 77

Part 4 The Compositional Patterns of Vertebrate Genomes 81

Chapter 1. The fish genomes 83

1.1 Compositional properties: a CsCl analysis 83

1.2 Compositional properties: a Cs[subscript 2]SO[subscript 4]/BAMD analysis 95

1.3 Compositional properties: an analysis of long sequences 96

1.4 Compositional properties of coding sequences and introns 98

1.5 Compositional correlations 98

Chapter 2. Amphibian genomes 99

Chapter 3. Reptilian genomes 103

Chapter 4. Avian genomes 111

Chapter 5. Mammalian genomes 113

Part 5 Sequence Distribution in the Vertebrate Genomes 121

Chapter 1. Gene distribution in the vertebrate genome 123

1.1 The distribution of genes in the human genome: the two gene spaces 123

1.2 Properties of the two gene spaces 125

1.3 The distribution of genes in the vertebrate genomes 129

Chapter 2. The distribution of CpG islands in the vertebrate genome 131

Chapter 3. The distribution of CpG doublets and methylation in the vertebrate genome 135

3.1 CpG doublets 135

3.2 Two different CpG levels in vertebrate genomes 137

3.3 Two different methylation levels in vertebrate genomes 138

Part 6 The Distribution of Integrated Viral Sequences, Transposons and Duplicated Genes in the Mammalian Genome 147

Chapter 1. The distribution of proviruses in the mammalian genome 149

1.1 The integration of retroviral sequences into the mammalian genome 149

1.2 The bimodal compositional distribution of retroviral genomes 149

1.3 The localization of integrated viral sequences in the host genome 150

1.4 An analysis of integration sites near host cell genes 154

1.5 The correlation between the isochore localization of integrated retroviral sequences and their transcription 155

1.6 Integration in "open" chromatin and/or near CpG islands 156

1.7 The causes of the compartmentalized, "isopycnic" localization of viral sequences 158

Chapter 2. The distribution of repeated sequences in the mammalian genome 161

2.1 Alu and LINE repeats in human isochores 161

2.2 The evolutionary origin of repeat distribution: different viewpoints 166

2.3 Repeated sequences in coding sequences? 170

Chapter 3. The distribution of duplicated genes in the human genome 173

Part 7 The Organization of Chromosomes in Vertebrates 177

Chapter 1. Isochores and chromosomal bands 179

Chapter 2. Compositional mapping 181

2.1 Compositional mapping based on physical maps 181

2.2 Chromosomal compositional mapping at a 400-band resolution 184

2.3 Chromosomal compositional mapping at a 850-band resolution 187

Chapter 3. Genes, isochores and bands in human chromosomes 21 and 22 195

Chapter 4. Replication timing, recombination and transcription of chromosomal bands 201

4.1 Replication timing of R and G bands 201

4.2 Recombination in chromosomes 204

4.3 Transcription of chromosomal bands 206

Chapter 5. Isochores in the interphase nucleus 209

5.1 Distribution of the GC-richest and GC-poorest isochores in the interphase nucleus of human and chicken 209

5.2 Different compaction of the human GC-richest and GC-poorest chromosomal regions in interphase nuclei 209

5.3 The spatial distribution of genes in interphase nuclei 213

Part 8 The Organization of Plant Genomes 217

Chapter 1. The organization of the nuclear genome of plants 219

Chapter 2. Two classes of genes in plants 225

Chapter 3. Gene distribution in the genomes of plants 227

3.1 The gene space in the genomes of Gramineae 227

3.2 Misunderstandings about the gene space of Gramineae 231

3.3 The gene space of other plants 233

3.4 Distribution of genes in the genome of Arabidopsis 234

3.5 A comparison of the genomes of Arabidopsis and Gramineae 236

3.6 The bimodal gene distribution in the tobacco genome 239

3.7 Methylation patterns in the nuclear genomes of plants 239

Part 9 The Compositional Patterns of the Genomes of Invertebrates, Unicellular Eukaryotes and Prokaryotes 241

Chapter 1. The genome of a Urochordate, Ciona intestinalis 243

Chapter 2. The genome of Drosophila melanogaster 247

Chapter 3. The genome of Caenorhabditis elegans 251

Chapter 4. The nuclear genome of unicellular eukaryotes 253

Chapter 5. Compositional heterogeneity in prokaryotic genomes 257

5.1 CsCl gradient ultracentrifugation and traditional fixed-length window analysis 257

5.2 Generalized fixed-length window approaches 257

5.3 Intrinsic segmentation methods 259

5.4 Does intragenomic heterogeneity in E. coli arise from exogenous or endogenous DNA? 262

5.5 Inter- and intra-genomic GC distributions 263

Part 10 Gene Composition and Protein Structure 265

Chapter 1. The universal correlations 267

Chapter 2. The universal correlations and the hydrophobicity of proteins 271

Chapter 3. The universal correlation and imaginary genes 279

Chapter 4. Compositional gene landscapes 281

4.1 Large-scale-features of the human gene landscape 281

4.2 Gene landscapes correspond to protein landscapes 283

4.3 Gene landscapes correspond to experimentally determined DNA landscapes 283

Chapter 5. Nucleotide substitutions and composition in coding sequences.

Correlations with protein structure 285

5.1 Synonymous and nonsynonymous substitution rates in mammalian genes are correlated with each other 285

5.2 Synonymous and nonsynonymous substitution rates are correlated with protein structure 287

5.3 Synonymous and nonsynonymous substitution rates are correlated with protein structure: an intragenic analysis of the Leishmania GP63 genes 287

5.4 Base compositions at nonsynonymous positions are correlated with protein structure and with the genetic code 288

5.5 Base composition at synonymous positions are correlated with protein structure 291

Part 11 The Compositional Evolution of Vertebrate Genomes 293

Chapter 1. Two modes of evolution in vertebrates 295

Chapter 2. The maintenance of compositional patterns 297

2.1 The maintenance of the compositional patterns of warm-blooded vertebrates 297

2.2 The conservative mode of evolution and codon usage 298

2.3 Mutational biases in the human genome 300

Chapter 3. The two major compositional shifts in vertebrate genomes 303

3.2 Compositional constraints and codon usage 310

3.3 Other changes accompanying the major shifts 313

Chapter 4. The minor shift of murids 317

4.1 Differences in the compositional patterns of murids and other mammals 317

4.2 Isochore conservation in the MHC loci of human and mouse 318

4.3 The increased mutational input in murids 322

Chapter 5. The whole-genome shifts of vertebrates 323

Part 12 Natural Selection and Genetic Drift in Genome Evolution: The Neo-Selectionist Model 325

Chapter 1. Molecular evolution theories and vertebrate genomics 327

1.1 Molecular evolution theories 327

1.2 Structural genomics of vertebrates 329

1.3 Our previous conclusions 331

Chapter 2. Natural selection in the maintenance of compositional patterns of vertebrate genomes: the neo-selectionist model 333

Chapter 3. Natural selection in the major shifts 337

Chapter 4. The causes of the major shifts 339

4.1 Compositional changes and natural selection 339

4.2 The thermodynamic stability hypothesis: DNA results 340

4.3 The thermodynamic stability hypothesis: RNA results 347

4.4 The thermodynamic stability hypothesis: Protein results 347

4.5 The primum movens problem 351

Chapter 5. Objections to selection 353

Chapter 6. Alternative explanations for the major shifts 361

Chapter 7. Natural selection and the "whole genome" shifts of prokaryotes and eukaryotes 367

Recapitulation 369

1. Structural genomics of warm-blooded vertebrates 370

2. Chromosomes and interphase nuclei 374

3. Comparative and evolutionary genomics of vertebrates 375

4. The eukaryotic genome 382

5. The prokaryotic genome 383.

Notes:

Includes bibliographical references (pages 391-434).

ISBN:

0444512551

OCLC:

55120974