Somatic Genome Variation: in Animals, Plants, and Microorganisms

Somatic Genome Variation: in Animals, Plants, and Microorganisms

By: Xiu-Qing Li (editor)Hardback

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Description

Written by an international team of experts, Somatic Genome Variation presents a timely summary of the latest understanding of somatic genome development and variation in plants, animals, and microorganisms. Wide-ranging in coverage, the authors provide an updated view of somatic genomes and genetic theories while also offering interpretations of somatic genome variation. The text provides geneticists, bioinformaticians, biologist, plant scientists, crop scientists, and microbiologists with a valuable overview of this fascinating field of research.

About Author

About the Editor Xiu-Qing Li, Doctorat d'Etat 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.

Contents

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 3Jennifer 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 45Jeramiah 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 55Paola 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 77Christopher 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 91Andrey 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 103Gregory 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 119Eric Zampini, Sebastien Truche, Etienne 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 167John 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 199Adrianna 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 253Xiu-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 267Xiu-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 291Xiu ]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 299Xiu-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 309Xiu ]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 337Xiu-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 351Xiu-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 363Xiu ]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 377Xiu-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

Product Details

  • ISBN13: 9781118647066
  • Format: Hardback
  • Number Of Pages: 448
  • ID: 9781118647066
  • weight: 1052
  • ISBN10: 1118647068

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