List of Contributors xv Preface and Introduction xix Acknowledgments xxi About the Editor xxiii Part I Somatic Genome Variation in Animals and Humans 1 1 Polyploidy in Animal Development and Disease 3 Jennifer L. Bandura and Norman Zielke 1.1 Introduction 3 1.2 Mechanisms Inducing Somatic Polyploidy 4 1.3 The Core Cell Cycle Machinery 8 1.4 Genomic Organization of Polyploid Cells 9 1.5 Endoreplication: An Effective Tool for Post-Mitotic Growth and Tissue Regeneration 10 1.6 Initiation of Endoreplication in Drosophila 11 1.

7 Mechanisms of Endocycle Oscillations in Drosophila 15 1.8 Gene Amplification in Drosophila Follicle Cells 17 1.9 Endocycle Entry in the Trophoblast Lineage 19 1.10 Mechanisms of Endocycle Oscillations in Trophoblast Giant Cells 22 1.11 Cardiomyocytes 23 1.12 Hepatocytes 25 1.13 Megakaryocytes 28 1.14 Concluding Remarks 30 Acknowledgments 31 References 31 2 Large-Scale Programmed Genome Rearrangements in Vertebrates 45 Jeramiah J.

Smith 2.1 Introduction 45 2.1 Hagfish 46 2.3 Sea Lamprey 48 2.4 Zebra Finch 48 2.5 Emerging Themes and Directions 49 References 51 3 Chromosome Instability in Stem Cells 55 Paola Rebuzzini, Maurizio Zuccotti, Carlo Alberto Redi and Silvia Garagna 3.1 Introduction 55 3.2 Pluripotent Stem Cells 56 3.

3 Somatic Stem Cells 58 3.4 Mechanisms of Chromosomal Instability 59 3.5 Mechanisms of Chromosomal Instability in Stem Cells 63 References 63 Part II Somatic Genome Variation in Plants 75 4 Mechanisms of Induced Inheritable Genome Variation in Flax 77 Christopher A. Cullis 4.1 Introduction 77 4.2 Restructuring the Flax Genome 79 4.3 Specific Genomic Changes 80 4.4 What Happens When Plastic Plants Respond to Environmental Stresses? 83 4.

5 When Do the Genomic Changes Occur and Are they Adaptive? 83 4.6 Is this Genomic Response of Flax Unique? 84 4.7 Concluding Remarks 87 Acknowledgments 87 References 87 5 Environmentally Induced Genome Instability and its Inheritance 91 Andrey Golubov 5.1 Introduction 91 5.2 Stress and its Effects on Genomes 92 5.3 Transgenerational Inheritance 96 5.4 Concluding Remarks 97 Acknowledgments 97 References 97 6 The Mitochondrial Genome, Genomic Shifting, and Genomic Conflict 103 Gregory G. Brown 6.

1 Introduction 103 6.2 Heteroplasmy and Sublimons 105 6.3 Cytoplasmic Male Sterility (CMS) in Plants 108 6.4 Mitochondrial Sublimons and CMS 109 6.5 Restorer Gene Evolution: Somatic Genetic Changes Drive Nuclear Gene Diversity? 111 6.6 Concluding Remarks 112 References 113 7 Plastid Genome Stability and Repair 119 Éric Zampini, Sébastien Truche, Étienne Lepage, Samuel Tremblay?]Belzile and Normand Brisson 7.1 Introduction 120 7.2 Characteristics of the Plastid Genome 121 7.

3 Replication of Plastid DNA 124 7.4 Transcription in the Plastid 130 7.5 The Influence of Replication and Transcription on Plastid Genome Stability 131 7.6 Plastid Genome Stability and DNA Repair 133 7.7 Outcomes of DNA Rearrangements 145 7.8 Concluding Remarks 147 References 148 Part III Somatic Genome Variation in Microorganisms 165 8 RNA-Mediated Somatic Genome Rearrangement in Ciliates 167 John R. Bracht 8.1 Introduction 168 8.

2 Ciliates: Ubiquitous Eukaryotic Microorganisms with a Long Scientific History 168 8.3 Two''s Company: Nuclear Dimorphism in Ciliates 170 8.4 Paramecium: Non-Mendelian Inheritance Comes to Light 171 8.5 Tetrahymena and the Origin of the scanRNA Model 173 8.6 Small RNAs in Stylonychia and Oxytricha 175 8.7 Long Noncoding RNA Templates in Genome Rearrangement 176 8.8 Long Noncoding RNA: An Interface for Short Noncoding RNA 177 8.9 Short RNA-Mediated Heterochromatin Formation and DNA Elimination 179 8.

10 Transposable Elements and the Origins of Genome Rearrangements 182 8.11 Transposons, Phase Variation, and Programmed Genome Engineering in Bacteria 185 8.12 Transposases, Noncoding RNA, and Chromatin Modifications in VDJ Recombination of Vertebrates 186 8.13 Concluding Remarks: Ubiquitous Genome Variation, Transposons, and Noncoding RNA 187 Acknowledgments 187 References 187 9 Mitotic Genome Variations in Yeast and Other Fungi 199 Adrianna Skoneczna and Marek Skoneczny 9.1 Introduction 199 9.2 The Replication Process as a Possible Source of Genome Instability 200 9.3 Post-Replicative Repair (PRR) or Homologous Recombination (HR) Are Responsible for Error-Free and Error-Prone Repair of Blocking Lesions and Replication Stall-Borne Problems 219 9.4 Ploidy Maintenance and Chromosome Integrity Mechanisms 229 9.

5 Concluding Remarks 234 References 235 Part IV General Genome Biology 251 10 Genome Variation in Archaeans, Bacteria, and Asexually Reproducing Eukaryotes 253 Xiu-Qing Li 10.1 Introduction 254 10.2 Chromosome Number in Prokaryote Species 254 10.3 Genome Size Variation in Archaeans and Bacteria 255 10.4 Archaeal and Bacterial Genome Size Distribution 256 10.5 Genomic GC Content in Archaeans, Bacteria, Fungi, Protists, Plants, and Animals 257 10.6 Correlation between GC Content and Genome or Chromosome Size 259 10.7 Genome Size and GC-Content Variation in Primarily Asexually Reproducing Fungi 260 10.

8 Variation of Gene Direction 263 10.9 Concluding Remarks 263 Acknowledgments 264 References 264 11 RNA Polyadenylation Site Regions: Highly Similar in Base Composition Pattern but Diverse in Sequence--A Combination Ensuring Similar Function but Avoiding Repetitive-Regions-Related Genomic Instability 267 Xiu-Qing Li and Donglei Du 11.1 General Introduction to Gene Number, Direction, and RNA Polyadenylation 268 11.2 Base Selection at the Poly(A) Tail Starting Position 269 11.3 Most Frequent Upstream Motifs in Microorganisms, Plants, and Animals 271 11.4 Motif Frequencies in the Whole Genome 273 11.5 The Top 20 Hexamer Motifs in the Poly(A) Site Region in Humans 273 11.6 Polyadenylation Signal Motif Distribution 273 11.

7 Alternative Polyadenylation 275 11.8 Base Composition of 3'UTR in Plants and Animals 276 11.9 Base Composition Comparison between 3'UTR and Whole Genome 276 11.10 Base Composition of 3'COR in Plants and Animals 277 11.11 Base Composition Pattern of the Poly(A) Site Region in Protists 278 11.12 Base Composition Pattern of the Poly(A) Site Region in Plants 280 11.13 Base Composition Pattern of the Poly(A) Site Region in Animals 280 11.14 Comparison of Poly(A) Site Region Base Composition Patterns in Plants and Animals 280 11.

15 Common U-A-U-A-U Base Abundance Pattern in the Poly(A) Site Region in Fungi, Plants, and Animals 284 11.16 Difference between the Most Frequent Motifs and Seqlogo-Showed Most Frequent Bases 284 11.17 RNA Structure of the Poly(A) Site Region 286 11.18 Low Conservation in the Overall Nucleotide Sequence of the Poly(A) Site Region 286 11.19 Poly(A) Site Region Stability and Somatic Genome Variation 286 11.20 Concluding Remarks 287 Acknowledgments 288 References 288 12 Insulin Signaling Pathways in Humans and Plants 291 Xiu?]Qing Li and Tim Xing 12.1 Introduction 291 12.2 Ranking of the Insulin Signaling Pathway and its Key Proteins 293 12.

3 Diseases Caused by Somatic Mutations of the PI3K, PTEN, and AKT Proteins in the Insulin Signaling Pathway 293 12.4 Plant Insulin and Medical Use 295 12.5 Role of the Insulin Signaling Pathway in Regulating Plant Growth 295 12.6 Concluding Remarks 295 References 296 13 Developmental Variation in the Nuclear Genome Primary Sequence 299 Xiu-Qing Li 13.1 Introduction 299 13.2 Genetic Mutation, DNA Damage and Protection, and Gene Conversion in Somatic Cells 300 13.3 Programmed Large-Scale Variation in Primary DNA Sequences in Somatic Nuclear Genome 302 13.4 Generation of Antibody Genes in Animals through Somatic Genome Variation 303 13.

5 Developmental Variation in Primary DNA Sequences in the Somatic Cells of Plants 303 13.6 Heritability and Stability of Developmentally Induced Variation in the Somatic Nuclear Genome in Plants 303 13.7 Concluding Remarks 304 References 305 14 Ploidy Variation of the Nuclear, Chloroplast, and Mitochondrial Genomes in Somatic Cells 309 Xiu?]Qing Li, Benoit Bizimungu, Guodong Zhang and Huaijun Si 14.1 Introduction 310 14.2 Nuclear Genome in Somatic Cells 311 14.3 Plastid Genome Variation in Somatic Cells 317 14.4 Mitochondrial Genome in Somatic Cells 320 14.5 Organelle Genomes in Somatic Hybrids 324 14.

6 Effects of Nuclear Genome Ploidy on Organelle Genomes 325 14.7 Concluding Remarks 326 Acknowledgments 326 References 326 15 Molecular Mechanisms of Somatic Genome Variation 337 Xiu-Qing Li 15.1 Introduction 338 15.2 Mutation of Genes Involved in the Cell Cycle, Cell Division, or Centromere Function 338 15.3 DNA Damage 338.