Structural and evolutionary genomics: natural selection in genome evolution
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier
2004
|
| Schriftenreihe: | New comprehensive biochemistry
37 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XV, 434 S. Ill., zahlr. graph. Darst. |
| ISBN: | 0444512551 |
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XI
CONTENTS
PREFACE VII
PART 1: INTRODUCTION 1
1.1 THE GENOME: A SHORT HISTORY OF DIFFERENT VIEWS 3
1.2 POPULATION GENETICS AND MOLECULAR EVOLUTION 4
1.3 THREE REMARKS ON TERMINOLOGY 5
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 ORR PETITES 14 AND 26 39
2.7 TEMPERATURE AND THE REPLICATIVE ABILITY OF ORI~ 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 I 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
IMAGE 2
XII
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 2 SO 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 1 13
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 SE- QUENCES 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 SE- QUENCES 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
IMAGE 3
XIII
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, DONA INTESTINALIS 243
CHAPTER 2. THE GENOME OF DROSOPHILA METANOGASTER 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
ANA- LYSIS 257
5.2 GENERALIZED FIXED-LENGTH WINDOW APPROACHES 257
5.3 INTRINSIC SEGMENTATION METHODS 259
5.4 DOCS INTRAGENOMIC HETEROGENEITY IN E. COLI ARISE FROM EXOGENOUS OR
ENDO- GENOUS 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 HYDROPHOBIATY 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 285 PROTEIN STRUCTURE 5.1 SYNONYMOUS
AND NONSYNONYMOUS SUBSTITUTION RATES IN MAMMALIAN GENES ARE
CORRELATED WITH EACH OTHER 285
IMAGE 4
XIV
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
3.1 THE MAJOR SHIFTS 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 333 GENOMES: THE NEO-SELECTIONIST MODEL 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
IMAGE 5
XV
5. THE PROKARYOTIC GENOME 383
CONCLUSIONS 385
ABBREVIATIONS 389
REFERENCES 391
EXCEPT WHERE INDICATED OTHERWISE, ALL FIGURE LEGENDS ARE VERBATIM
TRANSCRIPTIONS OF THE ORIGINAL ONES.
|
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| series2 | New comprehensive biochemistry |
| spelling | Bernardi, Giorgio Verfasser aut Structural and evolutionary genomics natural selection in genome evolution Giorgio Bernardi Amsterdam [u.a.] Elsevier 2004 XV, 434 S. Ill., zahlr. graph. Darst. txt rdacontent n rdamedia nc rdacarrier New comprehensive biochemistry 37 Genom (DE-588)4156640-3 gnd rswk-swf Evolution (DE-588)4071050-6 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Wirbeltiere (DE-588)4066376-0 gnd rswk-swf Wirbeltiere (DE-588)4066376-0 s Genom (DE-588)4156640-3 s Evolution (DE-588)4071050-6 s DE-604 Phylogenie (DE-588)4076110-1 s b DE-604 New comprehensive biochemistry 37 (DE-604)BV000003914 37 SWB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012935746&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Bernardi, Giorgio Structural and evolutionary genomics natural selection in genome evolution New comprehensive biochemistry Genom (DE-588)4156640-3 gnd Evolution (DE-588)4071050-6 gnd Phylogenie (DE-588)4076110-1 gnd Wirbeltiere (DE-588)4066376-0 gnd |
| subject_GND | (DE-588)4156640-3 (DE-588)4071050-6 (DE-588)4076110-1 (DE-588)4066376-0 |
| title | Structural and evolutionary genomics natural selection in genome evolution |
| title_auth | Structural and evolutionary genomics natural selection in genome evolution |
| title_exact_search | Structural and evolutionary genomics natural selection in genome evolution |
| title_full | Structural and evolutionary genomics natural selection in genome evolution Giorgio Bernardi |
| title_fullStr | Structural and evolutionary genomics natural selection in genome evolution Giorgio Bernardi |
| title_full_unstemmed | Structural and evolutionary genomics natural selection in genome evolution Giorgio Bernardi |
| title_short | Structural and evolutionary genomics |
| title_sort | structural and evolutionary genomics natural selection in genome evolution |
| title_sub | natural selection in genome evolution |
| topic | Genom (DE-588)4156640-3 gnd Evolution (DE-588)4071050-6 gnd Phylogenie (DE-588)4076110-1 gnd Wirbeltiere (DE-588)4066376-0 gnd |
| topic_facet | Genom Evolution Phylogenie Wirbeltiere |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012935746&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000003914 |
| work_keys_str_mv | AT bernardigiorgio structuralandevolutionarygenomicsnaturalselectioningenomeevolution |