Somatic Genome Variation

About the Editor Xiu-Qing Li, Doctorat d'État en Sciences (France), is a senior level Research Scientist of Molecular Genetics at Agriculture and Agri-Food Canada (Government of Canada). Dr. Li is also an Adjunct Professor at the University of New Brunswick and serves as an editor on PloS ONE, Genetics and Epigeneitcs, and the Potato Journal.

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

15.4 Variation in Induction and Activity of Radical-Scavenging Enzymes 339

15.5 DNA Cytosine Deaminases 340

15.6 Variation in Protective Roles of Pigments against Oxidative Damage 340

15.7 RNA-Templated DNA Repair 341

15.8 Errors in DNA Repair 341

15.9 RNA-Mediated Somatic Genome Rearrangement 342

15.10 Repetitive DNA Instability 342

15.11 Extracellular DNA 343

15.12 DNA Transposition 343

15.13 Somatic Crossover and Gene Conversion 343

15.14 Molecular Heterosis 344

15.15 Genome Damage Induced by Endoplasmic Reticulum Stress 344

15.16 Telomere Degeneration 344

15.17 Concluding Remarks 344

References 345

16 Hypotheses for Interpreting Somatic Genome Variation 351
Xiu-Qing Li

16.1 Introduction 352

16.2 Cell-Specific Accumulation of Somatic Genome Variation in Somatic Cells 352

16.3 Developmental Age and Genomic Network of Reproductive Cells 353

16.4 Genome Generation Cycle of Species 353

16.5 Somatic Genome Variation and Tissue-Specific Requirements during Growth or Development 354

16.6 Costs and Benefits of Somatic Genome Variation 354

16.7 Hypothesis on the Existence of a Primitive Stage in both Animals and Plants 355

16.8 Sources of Genetic Variation from in Vitro Culture Propagation 357

16.9 Hypothesis that Heterosis Is Created by Somatic Genome Variation 357

16.10 Genome Stability through Structural Similarity and Sequence Dissimilarity 358

16.11 Hypothesis Interpreting the Maternal Transmission of Organelles 358

16.12 Ability of Humans to Deal with Somatic Genome Variation and Diseases 359

16.13 Concluding Remarks 360

References 360

17 Impacts of Somatic Genome Variation on Genetic Theories and Breeding Concepts, and the Distinction between Mendelian Genetic Variation, Somagenetic Variation, and Epigenetic Variation 363
Xiu]Qing Li

17.1 Introduction 364

17.2 The Term ‘Somatic Genome’ 365

17.3 Mendelian Genetic Variation, Epigenetic Variation, and Somagenetic Variation 365

17.4 What Is a Gene? 367

17.5 Breeding Criteria, Genome Cycle, Pure Lines, and Variety Stability 368

17.6 The Weismann Barrier Hypothesis and the Need for Revision 370

17.7 Implications for Species Evolution 370

17.8 Concluding Remarks 371

References 372

18 Somatic Genome Variation: What it Is and What it Means for Agriculture and Human Health 377
Xiu-Qing Li

18.1 Introduction 378

18.2 Natural Attributes of Somatic Genome Variation 378

18.3 Implications of Somatic Genome Variation for Human and Animal Health 380

18.4 Implications of Somatic Genome Variation for Agriculture 385

18.5 Concluding Remarks 391

Acknowledgments 392

References 392

Index 405