Cover -- Contents -- PREFACE -- INTRODUCTION -- The genome: a short history of different views -- Population genetics and molecular evolution -- Three remarks on terminology -- A brief chronology of our investigations -- Molecular approaches to the study of the genome -- LESSONS FROM A SMALL DISPENSABLE GENOME, THE MITOCHONDRIAL GENOME OF YEAST -- The mitochondrial genome of yeast and the petite mutation -- The "petite colonie" mutation -- The petite mutation is accompanied by gross alterations of mitochondrial DNA -- The AT spacers and the deletion hypothesis -- The petite mutation is due to large deletions -- The GC clusters -- The excision sites -- Genomes without genes -- The origins of replication -- Excision and recombination -- The canonical and the surrogate origins of replication of petite genomes -- The replication of petite genomes and the phenomenon of suppressivity -- The ori sequences as transcription initiation sites -- The effect of flanking sequences on the efficiency of replication of petite genomes -- The on petites 14 and 26 -- Temperature and the replicative ability of ori petites 14 and 26 -- The organization and evolution of the mitochondrial genome of yeast -- The organization of the mitochondrial genome of yeast -- The evolutionary origin of ori sequences -- The evolutionary origin of the GC clusters -- The evolutionary origin of the AT spacers and the var 1 gene -- The non-coding sequences: evolutionary origin and biological role -- THE ORGANIZATION OF THE VERTEBRATE GENOME -- Isochores and isochore families -- The fractionation of the bovine genome -- The fractionation of eukaryotic main-band DNAs -- Isochores and isochore families -- Isochores and the draft human genome sequence -- Other misunderstandings about isochores -- Compositional patterns of coding sequences.

Compositional correlations between coding and non-coding sequences -- THE COMPOSITIONAL PATTERNS OF VERTEBRATE GENOMES -- The fish genomes -- Compositional properties: a CsCl analysis -- Compositional properties: a Cs2SO4/BAMD analysis -- Compositional properties: an analysis of long sequences -- Compositional properties of coding sequences and introns -- Compositional correlations -- Amphibian genomes -- Reptilian genomes -- Avian genomes -- Mammalian genomes -- SEQUENCE DISTRIBUTION IN THE VERTEBRATE GENOMES -- Gene distribution in the vertebrate genome -- The distribution of genes in the human genome: the two gene spaces -- Properties of the two gene spaces -- The distribution of genes in the vertebrate genomes -- The distribution of CpG islands in the vertebrate genome -- The distribution of CpG doublets and methylation in the vertebrate genome -- CpG doublets -- Two different CpG levels in vertebrate genomes -- Two different methylation levels in vertebrate genomes -- THE DISTRIBUTION OF INTEGRATED VIRAL SEQUENCES, TRANSPOSONS AND DUPLICATED GENES IN THE MAMMALIAN GENOME -- The distribution of proviruses in the mammalian genome -- The integration of retro viral sequences into the mammalian genome -- The bimodal compositional distribution of retroviral genomes -- The localization of integrated viral sequences in the host genome -- An analysis of integration sites near host cell genes -- The correlation between the isochore localization of integrated retroviral sequences and their transcription -- Integration in "open" chromatin and/or near CpG islands -- The causes of the compartmentalized, "isopycnic" localization of viral sequences -- The distribution of repeated sequences in the mammalian genome -- Alu and LINE repeats in human isochores -- The evolutionary origin of repeat distribution: different viewpoints.

Repeated sequences in coding sequences? -- The distribution of duplicated genes in the human genome -- THE ORGANIZATION OF CHROMOSOMES IN VERTEBRATES -- Isochores and chromosomal bands -- Compositional mapping -- Compositional mapping based on physical maps -- Chromosomal compositional mapping at a 400-band resolution -- Chromosomal compositional mapping at a 850-band resolution -- Genes, isochores and bands in human chromosomes 21 and 22 -- Replication timing, recombination and transcription of chromosomal bands -- Replication timing of R and G bands -- Recombination in chromosomes -- Transcription of chromosomal bands -- Isochores in the interphase nucleus -- Distribution of the GC-richest and GC-poorest isochores in the interphase nucleus of human and chicken -- Different compaction of the human GC-richest and GC-poorest chromosomal regions in interphase nuclei -- The spatial distribution of genes in interphase nuclei -- THE ORGANIZATION OF PLANT GENOMES -- The organization of the nuclear genome of plants -- Two classes of genes in plants -- Gene distribution in the genomes of plants -- The gene space in the genomes of Gramineae -- Misunderstandings about the gene space of Gramineae -- The gene space of other plants -- Distribution of genes in the genome of Arabidopsis -- A comparison of the genomes of Arabidopsis and Gramineae -- The bimodal gene distribution in the tobacco genome -- Methylation patterns in the nuclear genomes of plants -- THE COMPOSITIONAL PATTERNS OF THE GENOMES OF INVERTEBRATES, UNICELLULAR EUKARYOTES AND PROKARYOTES -- The genome of a Urochordate, Ciona intestinalis -- The genome of Drosophila melanogaster -- The genome of Caenorhahditis elegans -- The nuclear genome of unicellular eukaryotes -- Compositional heterogeneity in prokaryotic genomes -- CsCl gradient ultracentrifugation and traditional fixed-length window analysis.

Generalized fixed-length window approaches -- Intrinsic segmentation methods -- Does intragenomic heterogeneity in E. coli arise from exogenous or endogenous DN A? -- Inter- and intra-genomic GC distributions -- GENE COMPOSITION AND PROTEIN STRUCTURE -- The universal correlations -- The universal correlations and the hydrophobicity of proteins -- The universal correlation and imaginary genes -- Compositional gene landscapes -- Large-scale-features of the human gene landscape -- Gene landscapes correspond to protein landscapes -- Gene landscapes correspond to experimentally determined DNA landscapes -- Nucleotide substitutions and composition in coding sequences. Correlations with protein structure -- Synonymous and nonsynonymous substitution rates in mammalian genes are correlated with each other -- Synonymous and nonsynonymous substitution rates are correlated with protein structure -- Synonymous and nonsynonymous substitution rates are correlated with protein structure: an intragenic analysis of the Leishmania GP63 genes -- Base compositions at nonsynonymous positions are correlated with protein structure and with the genetic code -- Base composition at synonymous positions are correlated with protein structure -- THE COMPOSITIONAL EVOLUTION OF VERTEBRATE GENOMES -- Two modes of evolution in vertebrates -- The maintenance of compositional patterns -- The maintenance of the compositional patterns of warm-blooded vertebrates -- The conservative mode of evolution and codon usage -- Mutational biases in the human genome -- The two major compositional shifts in vertebrate genomes -- The major shifts -- Compositional constraints and codon usage -- Other changes accompanying the major shifts -- The minor shift of murids -- Differences in the compositional patterns of murids and other mammals -- Isochore conservation in the MHC loci of human and mouse.

The increased mutational input in murids -- The whole-genome shifts of vertebrates -- NATURAL SELECTION AND GENETIC DRIFT IN GENOME EVOLUTION: THE NEO-SELECTIONIST MODEL -- Molecular evolution theories and vertebrate genomics -- Molecular evolution theories -- Structural genomics of vertebrates -- Our previous conclusions -- Natural selection in the maintenance of compositional patterns of vertebrate genomes: the neo-selectionist model -- Natural selection in the major shifts -- The causes of the major shifts -- Compositional changes and natural selection -- The thermodynamic stability hypothesis: DNA results -- The thermodynamic stability hypothesis: RNA results -- The thermodynamic stability hypothesis: Protein results -- The primum movens problem -- Objections to selection -- Alternative explanations for the major shifts -- Natural selection and the "whole genome" shifts of prokaryotes and eukaryotes -- RECAPITULATION -- Structural genomics of warm-blooded vertebrates -- Chromosomes and interphase nuclei -- Comparative and evolutionary genomics of vertebrates -- The eukaryotic genome -- The prokaryotic genome -- CONCLUSIONS -- Abbreviations -- References -- SUBJECT INDEX -- AN UPDATE.