Foreword xiii Bernard DUJON -- Introduction xv Guy-Franck RICHARD -- Chapter 1 Whole-Genome Duplications, a Source of Redundancy at the Entire-Genome Scale 1 Elise PAREY and Camille BERTHELOT -- 1.1 Prevalence of polyploids in the tree of life -- 1.1.1 Whole duplications in eukaryotes -- 1.1.2 Polyploidies in prokaryotic organisms -- 1.1.3 Polyploid cells in normal and pathological physiology -- 1.2 Mechanisms for the appearance of whole-genome duplications -- 1.2.1 Non-separation of chromosomes after replication -- 1.2.2 Autopolyploidization, a perfect genome redundancy -- 1.2.3 Allopolyploidization, an overlapping of genomes of similar species -- 1.3 Cellular consequences of whole-genome duplications -- 1.3.1 Disruption of cell and nucleus organization -- 1.3.2 Modifications in the expression of genes and transposons -- 1.3.3 Unstable meiosis -- 1.4 Rediploidization: evolutionary reduction in genetic redundancy -- 1.4.1 Resolution of meiosis by karyotype rearrangement -- 1.4.2 Evolutionary divergence of duplicated sequences -- 1.4.3 Bias and dominance during rediploidization -- 1.4.4 Incomplete and lineage-specific rediploidizations -- 1.5 Functions and evolution of duplicated genes -- 1.5.1 Redundancy and subfunctionalization -- 1.5.2 Neofunctionalization and evolutionary innovations -- 1.5.3 Gene repertoire bias -- 1.5.4 Regulatory blocks and splitting of regulatory regions -- 1.6 Whole-genome duplications and evolutionary diversification -- 1.6.1 Association with geological crises -- 1.6.2 Evolutionary speciations and radiations -- 1.7 Perspectives and conclusions -- 1.8 References -- Chapter 2 Segmental Duplications and CNVs: Adaptive Potential of Structural Polymorphism 47 Patricia BALARESQUE and Franklin DELEHELLE -- 2.1 The multiple facets of genetic polymorphism -- 2.2 From Segmental Duplications to Copy Number Variants: terminology -- 2.3 SDs: a general overview -- 2.3.1 Background -- 2.3.2 SDs: more than a category of sequences, superstructures -- 2.3.3 SD and CNV: study biases related to the attractiveness of subjects as well as to the technological developments of the moment -- 2.3.4 SD: characteristics in human and non-human primates -- 2.4 Methodologies for detecting structural variation in genomes -- 2.4.1 In vitro methods -- 2.4.2 Methods on reads -- 2.4.3 Post-assembly methods -- 2.5 The molecular mechanisms at the origin of structural variation -- 2.5.1 Homologous recombination mechanisms -- 2.5.2 Non-homologous recombination mechanisms -- 2.6 Regions rich in SDs/LCRs favor the creation of CNVs: insertions/duplications, deletions and inversions -- 2.6.1 Insertions/duplications and deletions -- 2.6.2 Inversions -- 2.7 From SDs to CNVs in humans and primates -- 2.7.1 General overview -- 2.7.2 Delineating regions of interest -- 2.7.3 Heterogeneity in the distribution of intra- and interchromosomal SDs -- 2.7.4 Intrachromosomal and interchromosomal SDs: what do they teach us about the evolutionary history and origin of SDs? -- 2.7.5 Intra- and interchromosomal SDs: the specific case of sex chromosomes -- 2.7.6 SDs: an association with specific sequences? -- 2.8 SDs in little-studied species: general genomic profiles -- 2.8.1 Twelve genomes under study -- 2.8.2 Distribution and characteristics of SDs in genomes -- 2.9 SD content: impact of a duplicated environment on sequences that make up the SDs -- 2.9.1 SDs and non-coding sequences: the case of microsatellites -- 2.9.2 SDs and coding genes: the fate of genes in SDs -- 2.10 SDs and epigenetic modifications -- 2.11 The adaptive potential of SDs: between the benefit of innovation and the cost of pathology -- 2.11.1 The organism's defense: immune system -- 2.11.2 Nutrient/food assimilation -- 2.11.3 Sensory perception of the environment -- 2.11.4 Neurological processes -- 2.11.5 Reproduction and the X and Y chromosomes: true SD concentrates -- 2.12 SDs and associated CNVs: their roles in species adaptation to changes in environments -- 2.12.1 SDs: a link between genomic architecture, adaptive potential and environmental changes? -- 2.12.2 Adaptation to global environmental stress -- 2.12.3 Adaptation to nutrient-poor surroundings -- 2.12.4 Adaptation to low and high temperatures -- 2.12.5 Heavy-metal adaptation -- 2.12.6 Antibiotics and drugs -- 2.12.7 Pesticide resistance -- 2.12.8 Domestication and post-domestication of plant and animal species -- 2.12.9 Competition and evolutionary success: invasive species and hybridization -- 2.13 Conclusion -- 2.14 Glossary of terms -- 2.15 References -- Chapter 3 Transposable Elements: Parasites that Shape Genome Evolution 117 Amandine BONNET, Karine CASIER, Clement CARRE, Laure TEYSSET and Pascale LESAGE -- 3.1 Transposable elements in eukaryotic genomes -- 3.1.1 TEs: essential components of eukaryotic genomes -- 3.1.2 Acquisition of new TEs by horizontal transfer -- 3.2 Classification of TEs and transposition mechanisms -- 3.2.1 Class I retrotransposons -- 3.2.2 Class II DNA transposons -- 3.3 TE self-regulation -- 3.3.1 Spatio-temporal regulation of TE expression -- 3.3.2 Self-regulation of transposition efficiency -- 3.3.3 Selective integration to better protect the genome -- 3.4 TE restriction by the host -- 3.4.1 Transcriptional repression of genomic copies -- 3.4.2 TE transcripts: choice targets for multiple restrictions -- 3.4.3 The Swiss knives of TE restriction: piRNAs -- 3.4.4 Reverse transcription of retroelements: a key step to inhibit -- 3.5 The impact of transposition events on genomes -- 3.5.1 The structural and functional consequences of TE activity on the genome -- 3.5.2 Pathologies associated with TE activity -- 3.5.3 The impact of TEs on the evolution of the host -- 3.6 Conclusion -- 3.7 References -- Chapter 4 Insights Into the Evolutionary Diversity of Centromeres 181 Nuria CORTES-SILVA, Aruni P SENARATNE and Ines A DRINNENBERG -- 4.1 The centromere -- 4.1.1 Definition and historical background -- 4.1.2 Two main types of centromeric architectures -- 4.2 Monocentromeres -- 4.2.1 The diversity of monocentric architectures across fungi -- 4.2.2 Animal and plant models contain long repetitive regional centromeres -- 4.3 Holocentromeres -- 4.3.1 Nematodes -- 4.3.2 Plants -- 4.3.3 Insects -- 4.4 Open questions -- 4.5 Acknowledgments -- 4.6 References -- Chapter 5 Evolution and Functions of Telomeres 207 Arturo LONDONO-VALLEJO -- 5.1 Primary structure of telomeres -- 5.1.1 Origin and evolution of telomeres -- 5.1.2 Nucleoprotein structure of telomeres -- 5.2 A telomere specific higher order structure: the T-loop -- 5.2.1 Telomere replication, a fundamental mechanism for telomere maintenance -- 5.3 Telomere lengthening mechanisms -- 5.4 Telomere length homeostasis -- 5.5 Telomeres and genome organization and function -- 5.6 Cell senescence, aging and disease -- 5.7 Conclusion -- 5.8 Acknowledgments -- 5.9 References -- Chapter 6 G-quadruplexes: Structure, Detection and Functions 239 Emilia Puig LOMBARDI -- 6.1 From guanine-guanine base-pairing to a secondary structure -- 6.1.1 G-quartets -- 6.1.2 Folding into a G-quadruplex structure -- 6.2 The G4 structure: variations on a theme -- 6.2.1 RNA G-quadruplexes (rG4) -- 6.2.2 Exceptions to the rule(s): non-canonical G-quadruplexes -- 6.3 Finding G-quadruplexes in a genome -- 6.3.1 Experimental methods for G-quadruplex detection -- 6.3.2 Computational methods -- 6.4 Biological roles of G-quadruplexes -- 6.4.1 First role attributed to quadruplexes: their formation -- telomeres -- 6.4.2 Predictions based on bioinformatic analyses -- 6.5 Perspective: G-quadruplexes as anticancer therapeutic targets -- 6.6 References -- Chapter 7 Satellite DNA, Microsatellites and Minisatellites 273 Wilhelm VAYSSE-ZINKHOFER and Guy-Franck RICHARD -- 7.1 Satellite DNAs, origin and definition -- 7.1.1 Minisatellites -- 7.1.2 Microsatellites -- 7.2 From semantics to biology -- 7.2.1 Distribution of satellite DNAs in genomes -- 7.2.2 Polymorphic genetic markers -- 7.2.3 Trinucleotide repeat expansions -- 7.2.4 Microsatellites regulate gene expression -- 7.2.5 Minisatellites are important in cell adhesion -- 7.2.6 Function of megasatellites -- 7.2.7 Centromeric satellite DNA, complexity of structure-function studies -- 7.3 The evolutionary mechanisms of tandem repeats -- 7.3.1 Historical model of slippage during replication -- 7.3.2 Slippage during DNA repair -- 7.3.3 Repeat expansions and contractions during homologous recombination -- 7.4 Microsatellites in human diseases -- 7.4.1

Triplet repeat expansion disorders -- 7.4.2 Colorectal cancers and the mismatch repair system -- 7.4.3 Fragile sites -- 7.5 De novo fo.

rmation and evolution of tandem repeats -- 7.5.1 Birth and death of microsatellites -- 7.5.2 Formation of minisatellites -- 7.6 Perspectives -- 7.6.1 Inadequacy of software tools -- 7.6.2 The importance of definitions in biology -- 7.7 Acknowledgments -- 7.8 References -- Chapter 8 CRISPR-Cas: An Adaptive Immune System 319 Marie TOUCHON -- 8.1 A brief history of the discovery of CRISPR-Cas systems -- 8.2 General characteristics of CRISPR-Cas systems -- 8.2.1 Diversity of repeats -- 8.2.2 Diversity and origin of spacers -- 8.2.3 Diversity and evolutionary classification of cas genes -- 8.2.4 Origin of CRISPR-Cas systems -- 8.3 Evolution of CRISPR-Cas systems -- 8.3.1 Scattered distribution of CRISPR-Cas systems -- 8.3.2 Massive transfer of CRISPR-Cas systems -- 8.3.3 Commonly lost systems -- 8.3.4 Evolutionary dynamics of CRISPR arrays -- 8.4 An adaptive immune system -- 8.4.1 A three-stage immune response -- 8.4.2 Diversity of CRISPR-Cas molecular mechanisms -- 8.4.3 Self- and none self-discrimination: avoiding self-targeting by CRISPR -- 8.5 Phage escape mechanisms -- 8.5.1 Genomic modifications -- 8.5.2 Anti-CRISPR proteins -- 8.6 Biological cost of CRISPR-Cas systems -- 8.6.1 Cost of expression -- 8.6.2 Cost of autoimmunity -- 8.6.3 The genetic background of the host -- 8.6.4 Limiting horizontal gene transfer -- 8.6.5 Naive and primed adaptation -- 8.7 Importance in nature: impact of ecological factors -- 8.7.1 Phage diversity - mutation rate -- 8.7.2 Phage diversity - population size -- 8.7.3 Infectious risk - alternative strategies -- 8.8 Conclusions and perspectives -- 8.9 References -- List of Authors -- Index.