Somatic Genome Variation

About the EditorXiu-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 xvPreface and Introduction xixAcknowledgments xxiAbout the Editor xxiiiPart I Somatic Genome Variation in Animals and Humans 11 Polyploidy in Animal Development and Disease 3Jennifer L. Bandura and Norman Zielke1.1 Introduction 31.2 Mechanisms Inducing Somatic Polyploidy 41.3 The Core Cell Cycle Machinery 81.4 Genomic Organization of Polyploid Cells 91.5 Endoreplication: An Effective Tool for Post-Mitotic Growth and Tissue Regeneration 101.6 Initiation of Endoreplication in Drosophila 111.7 Mechanisms of Endocycle Oscillations in Drosophila 151.8 Gene Amplification in Drosophila Follicle Cells 171.9 Endocycle Entry in the Trophoblast Lineage 191.10 Mechanisms of Endocycle Oscillations in Trophoblast Giant Cells 221.11 Cardiomyocytes 231.12 Hepatocytes 251.13 Megakaryocytes 281.14 Concluding Remarks 30Acknowledgments 31References 312 Large-Scale Programmed Genome Rearrangements in Vertebrates 45Jeramiah J. Smith2.1 Introduction 452.1 Hagfish 462.3 Sea Lamprey 482.4 Zebra Finch 482.5 Emerging Themes and Directions 49References 513 Chromosome Instability in Stem Cells 55Paola Rebuzzini, Maurizio Zuccotti, Carlo Alberto Redi and Silvia Garagna3.1 Introduction 553.2 Pluripotent Stem Cells 563.3 Somatic Stem Cells 583.4 Mechanisms of Chromosomal Instability 593.5 Mechanisms of Chromosomal Instability in Stem Cells 63References 63Part II Somatic Genome Variation in Plants 754 Mechanisms of Induced Inheritable Genome Variation in Flax 77Christopher A. Cullis4.1 Introduction 774.2 Restructuring the Flax Genome 794.3 Specific Genomic Changes 804.4 What Happens When Plastic Plants Respond to Environmental Stresses? 834.5 When Do the Genomic Changes Occur and Are they Adaptive? 834.6 Is this Genomic Response of Flax Unique? 844.7 Concluding Remarks 87Acknowledgments 87References 875 Environmentally Induced Genome Instability and its Inheritance 91Andrey Golubov5.1 Introduction 915.2 Stress and its Effects on Genomes 925.3 Transgenerational Inheritance 965.4 Concluding Remarks 97Acknowledgments 97References 976 The Mitochondrial Genome, Genomic Shifting, and Genomic Conflict 103Gregory G. Brown6.1 Introduction 1036.2 Heteroplasmy and Sublimons 1056.3 Cytoplasmic Male Sterility (CMS) in Plants 1086.4 Mitochondrial Sublimons and CMS 1096.5 Restorer Gene Evolution: Somatic Genetic Changes Drive Nuclear Gene Diversity? 1116.6 Concluding Remarks 112References 1137 Plastid Genome Stability and Repair 119Éric Zampini, Sébastien Truche, Étienne Lepage, Samuel Tremblay]Belzile and Normand Brisson7.1 Introduction 1207.2 Characteristics of the Plastid Genome 1217.3 Replication of Plastid DNA 1247.4 Transcription in the Plastid 1307.5 The Influence of Replication and Transcription on Plastid Genome Stability 1317.6 Plastid Genome Stability and DNA Repair 1337.7 Outcomes of DNA Rearrangements 1457.8 Concluding Remarks 147References 148Part III Somatic Genome Variation in Microorganisms 1658 RNA-Mediated Somatic Genome Rearrangement in Ciliates 167John R. Bracht8.1 Introduction 1688.2 Ciliates: Ubiquitous Eukaryotic Microorganisms with a Long Scientific History 1688.3 Two’s Company: Nuclear Dimorphism in Ciliates 1708.4 Paramecium: Non-Mendelian Inheritance Comes to Light 1718.5 Tetrahymena and the Origin of the scanRNA Model 1738.6 Small RNAs in Stylonychia and Oxytricha 1758.7 Long Noncoding RNA Templates in Genome Rearrangement 1768.8 Long Noncoding RNA: An Interface for Short Noncoding RNA 1778.9 Short RNA-Mediated Heterochromatin Formation and DNA Elimination 1798.10 Transposable Elements and the Origins of Genome Rearrangements 1828.11 Transposons, Phase Variation, and Programmed Genome Engineering in Bacteria 1858.12 Transposases, Noncoding RNA, and Chromatin Modifications in VDJ Recombination of Vertebrates 1868.13 Concluding Remarks: Ubiquitous Genome Variation, Transposons, and Noncoding RNA 187Acknowledgments 187References 1879 Mitotic Genome Variations in Yeast and Other Fungi 199Adrianna Skoneczna and Marek Skoneczny9.1 Introduction 1999.2 The Replication Process as a Possible Source of Genome Instability 2009.3 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 2199.4 Ploidy Maintenance and Chromosome Integrity Mechanisms 2299.5 Concluding Remarks 234References 235Part IV General Genome Biology 25110 Genome Variation in Archaeans, Bacteria, and Asexually Reproducing Eukaryotes 253Xiu-Qing Li10.1 Introduction 25410.2 Chromosome Number in Prokaryote Species 25410.3 Genome Size Variation in Archaeans and Bacteria 25510.4 Archaeal and Bacterial Genome Size Distribution 25610.5 Genomic GC Content in Archaeans, Bacteria, Fungi, Protists, Plants, and Animals 25710.6 Correlation between GC Content and Genome or Chromosome Size 25910.7 Genome Size and GC-Content Variation in Primarily Asexually Reproducing Fungi 26010.8 Variation of Gene Direction 26310.9 Concluding Remarks 263Acknowledgments 264References 26411 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 Du11.1 General Introduction to Gene Number, Direction, and RNA Polyadenylation 26811.2 Base Selection at the Poly(A) Tail Starting Position 26911.3 Most Frequent Upstream Motifs in Microorganisms, Plants, and Animals 27111.4 Motif Frequencies in the Whole Genome 27311.5 The Top 20 Hexamer Motifs in the Poly(A) Site Region in Humans 27311.6 Polyadenylation Signal Motif Distribution 27311.7 Alternative Polyadenylation 27511.8 Base Composition of 3′UTR in Plants and Animals 27611.9 Base Composition Comparison between 3′UTR and Whole Genome 27611.10 Base Composition of 3′COR in Plants and Animals 27711.11 Base Composition Pattern of the Poly(A) Site Region in Protists 27811.12 Base Composition Pattern of the Poly(A) Site Region in Plants 28011.13 Base Composition Pattern of the Poly(A) Site Region in Animals 28011.14 Comparison of Poly(A) Site Region Base Composition Patterns in Plants and Animals 28011.15 Common U-A-U-A-U Base Abundance Pattern in the Poly(A) Site Region in Fungi, Plants, and Animals 28411.16 Difference between the Most Frequent Motifs and Seqlogo-Showed Most Frequent Bases 28411.17 RNA Structure of the Poly(A) Site Region 28611.18 Low Conservation in the Overall Nucleotide Sequence of the Poly(A) Site Region 28611.19 Poly(A) Site Region Stability and Somatic Genome Variation 28611.20 Concluding Remarks 287Acknowledgments 288References 28812 Insulin Signaling Pathways in Humans and Plants 291Xiu]Qing Li and Tim Xing12.1 Introduction 29112.2 Ranking of the Insulin Signaling Pathway and its Key Proteins 29312.3 Diseases Caused by Somatic Mutations of the PI3K, PTEN, and AKT Proteins in the Insulin Signaling Pathway 29312.4 Plant Insulin and Medical Use 29512.5 Role of the Insulin Signaling Pathway in Regulating Plant Growth 29512.6 Concluding Remarks 295References 29613 Developmental Variation in the Nuclear Genome Primary Sequence 299Xiu-Qing Li13.1 Introduction 29913.2 Genetic Mutation, DNA Damage and Protection, and Gene Conversion in Somatic Cells 30013.3 Programmed Large-Scale Variation in Primary DNA Sequences in Somatic Nuclear Genome 30213.4 Generation of Antibody Genes in Animals through Somatic Genome Variation 30313.5 Developmental Variation in Primary DNA Sequences in the Somatic Cells of Plants 30313.6 Heritability and Stability of Developmentally Induced Variation in the Somatic Nuclear Genome in Plants 30313.7 Concluding Remarks 304References 30514 Ploidy Variation of the Nuclear, Chloroplast, and Mitochondrial Genomes in Somatic Cells 309Xiu]Qing Li, Benoit Bizimungu, Guodong Zhang and Huaijun Si14.1 Introduction 31014.2 Nuclear Genome in Somatic Cells 31114.3 Plastid Genome Variation in Somatic Cells 31714.4 Mitochondrial Genome in Somatic Cells 32014.5 Organelle Genomes in Somatic Hybrids 32414.6 Effects of Nuclear Genome Ploidy on Organelle Genomes 32514.7 Concluding Remarks 326Acknowledgments 326References 32615 Molecular Mechanisms of Somatic Genome Variation 337Xiu-Qing Li15.1 Introduction 33815.2 Mutation of Genes Involved in the Cell Cycle, Cell Division, or Centromere Function 33815.3 DNA Damage 33815.4 Variation in Induction and Activity of Radical-Scavenging Enzymes 33915.5 DNA Cytosine Deaminases 34015.6 Variation in Protective Roles of Pigments against Oxidative Damage 34015.7 RNA-Templated DNA Repair 34115.8 Errors in DNA Repair 34115.9 RNA-Mediated Somatic Genome Rearrangement 34215.10 Repetitive DNA Instability 34215.11 Extracellular DNA 34315.12 DNA Transposition 34315.13 Somatic Crossover and Gene Conversion 34315.14 Molecular Heterosis 34415.15 Genome Damage Induced by Endoplasmic Reticulum Stress 34415.16 Telomere Degeneration 34415.17 Concluding Remarks 344References 34516 Hypotheses for Interpreting Somatic Genome Variation 351Xiu-Qing Li16.1 Introduction 35216.2 Cell-Specific Accumulation of Somatic Genome Variation in Somatic Cells 35216.3 Developmental Age and Genomic Network of Reproductive Cells 35316.4 Genome Generation Cycle of Species 35316.5 Somatic Genome Variation and Tissue-Specific Requirements during Growth or Development 35416.6 Costs and Benefits of Somatic Genome Variation 35416.7 Hypothesis on the Existence of a Primitive Stage in both Animals and Plants 35516.8 Sources of Genetic Variation from in Vitro Culture Propagation 35716.9 Hypothesis that Heterosis Is Created by Somatic Genome Variation 35716.10 Genome Stability through Structural Similarity and Sequence Dissimilarity 35816.11 Hypothesis Interpreting the Maternal Transmission of Organelles 35816.12 Ability of Humans to Deal with Somatic Genome Variation and Diseases 35916.13 Concluding Remarks 360References 36017 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 Li17.1 Introduction 36417.2 The Term ‘Somatic Genome’ 36517.3 Mendelian Genetic Variation, Epigenetic Variation, and Somagenetic Variation 36517.4 What Is a Gene? 36717.5 Breeding Criteria, Genome Cycle, Pure Lines, and Variety Stability 36817.6 The Weismann Barrier Hypothesis and the Need for Revision 37017.7 Implications for Species Evolution 37017.8 Concluding Remarks 371References 37218 Somatic Genome Variation: What it Is and What it Means for Agriculture and Human Health 377Xiu-Qing Li18.1 Introduction 37818.2 Natural Attributes of Somatic Genome Variation 37818.3 Implications of Somatic Genome Variation for Human and Animal Health 38018.4 Implications of Somatic Genome Variation for Agriculture 38518.5 Concluding Remarks 391Acknowledgments 392References 392Index 405