Somatic Genome Variation E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 988

Veröffentlichungsjahr: 2017

Beschreibung

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.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

List of Contributors

Preface and Introduction

Acknowledgments

About the Editor

Part I: Somatic Genome Variation in Animals and Humans

Chapter 1: Polyploidy in Animal Development and Disease

1.1 Introduction

1.2 Mechanisms Inducing Somatic Polyploidy

1.3 The Core Cell Cycle Machinery

1.4 Genomic Organization of Polyploid Cells

1.5 Endoreplication: An Effective Tool for Post-Mitotic Growth and Tissue Regeneration

1.6 Initiation of Endoreplication in

Drosophila

1.7 Mechanisms of Endocycle Oscillations in

Drosophila

1.8 Gene Amplification in

Drosophila

Follicle Cells

1.9 Endocycle Entry in the Trophoblast Lineage

1.10 Mechanisms of Endocycle Oscillations in Trophoblast Giant Cells

1.11 Cardiomyocytes

1.12 Hepatocytes

1.13 Megakaryocytes

1.14 Concluding Remarks

Acknowledgments

References

Chapter 2: Large-Scale Programmed Genome Rearrangements in Vertebrates

2.1 Introduction

2.1 Hagfish

2.3 Sea Lamprey

2.4 Zebra Finch

2.5 Emerging Themes and Directions

References

Chapter 3: Chromosome Instability in Stem Cells

3.1 Introduction

3.2 Pluripotent Stem Cells

3.3 Somatic Stem Cells

3.3.1 Mesenchymal Stem Cells

3.4 Mechanisms of Chromosomal Instability

3.5 Mechanisms of Chromosomal Instability in Stem Cells

References

Part II: Somatic Genome Variation in Plants

Chapter 4: Mechanisms of Induced Inheritable Genome Variation in Flax

4.1 Introduction

4.2 Restructuring the Flax Genome

4.3 Specific Genomic Changes

4.4 What Happens When Plastic Plants Respond to Environmental Stresses?

4.5 When Do the Genomic Changes Occur and Are they Adaptive?

4.6 Is this Genomic Response of Flax Unique?

4.7 Concluding Remarks

Acknowledgments

References

Chapter 5: Environmentally Induced Genome Instability and its Inheritance

5.1 Introduction

5.2 Stress and its Effects on Genomes

5.3 Transgenerational Inheritance

5.4 Concluding Remarks

Acknowledgments

References

Chapter 6: The Mitochondrial Genome, Genomic Shifting, and Genomic Conflict

6.1 Introduction

6.2 Heteroplasmy and Sublimons

6.3 Cytoplasmic Male Sterility (CMS) in Plants

6.4 Mitochondrial Sublimons and CMS

6.5 Restorer Gene Evolution: Somatic Genetic Changes Drive Nuclear Gene Diversity?

6.6 Concluding Remarks

References

Chapter 7: Plastid Genome Stability and Repair

7.1 Introduction

7.2 Characteristics of the Plastid Genome

7.3 Replication of Plastid DNA

7.4 Transcription in the Plastid

7.5 The Influence of Replication and Transcription on Plastid Genome Stability

7.6 Plastid Genome Stability and DNA Repair

7.7 Outcomes of DNA Rearrangements

7.8 Concluding Remarks

References

Part III: Somatic Genome Variation in Microorganisms

Chapter 8: RNA-Mediated Somatic Genome Rearrangement in Ciliates

8.1 Introduction

8.2 Ciliates: Ubiquitous Eukaryotic Microorganisms with a Long Scientific History

8.3 Two's Company: Nuclear Dimorphism in Ciliates

8.4

Paramecium

: Non-Mendelian Inheritance Comes to Light

8.5

Tetrahymena

and the Origin of the scanRNA Model

8.6 Small RNAs in

Stylonychia

and

Oxytricha

8.7 Long Noncoding RNA Templates in Genome Rearrangement

8.8 Long Noncoding RNA: An Interface for Short Noncoding RNA

8.9 Short RNA-Mediated Heterochromatin Formation and DNA Elimination

8.10 Transposable Elements and the Origins of Genome Rearrangements

8.11 Transposons, Phase Variation, and Programmed Genome Engineering in Bacteria

8.12 Transposases, Noncoding RNA, and Chromatin Modifications in VDJ Recombination of Vertebrates

8.13 Concluding Remarks: Ubiquitous Genome Variation, Transposons, and Noncoding RNA

Acknowledgments

References

Chapter 9: Mitotic Genome Variations in Yeast and Other Fungi

9.1 Introduction

9.2 The Replication Process as a Possible Source of Genome Instability

9.4 Ploidy Maintenance and Chromosome Integrity Mechanisms

9.5 Concluding Remarks

References

Webliography

Part IV: General Genome Biology

Chapter 10: General Genome Biology 10: Genome Variation in Archaeans, Bacteria, and Asexually Reproducing Eukaryotes

10.1 Introduction

10.2 Chromosome Number in Prokaryote Species

10.3 Genome Size Variation in Archaeans and Bacteria

10.4 Archaeal and Bacterial Genome Size Distribution

10.5 Genomic GC Content in Archaeans, Bacteria, Fungi, Protists, Plants, and Animals

10.6 Correlation between GC Content and Genome or Chromosome Size

10.7 Genome Size and GC-Content Variation in Primarily Asexually Reproducing Fungi

10.8 Variation of Gene Direction

10.9 Concluding Remarks

Acknowledgments

References

Chapter 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

11.1 General Introduction to Gene Number, Direction, and RNA Polyadenylation

11.2 Base Selection at the Poly(A) Tail Starting Position

11.3 Most Frequent Upstream Motifs in Microorganisms, Plants, and Animals

11.4 Motif Frequencies in the Whole Genome

11.5 The Top 20 Hexamer Motifs in the Poly(A) Site Region in Humans

11.6 Polyadenylation Signal Motif Distribution

11.7 Alternative Polyadenylation

11.8 Base Composition of 3′UTR in Plants and Animals

11.9 Base Composition Comparison between 3′UTR and Whole Genome

11.10 Base Composition of 3′COR in Plants and Animals

11.11 Base Composition Pattern of the Poly(A) Site Region in Protists

11.12 Base Composition Pattern of the Poly(A) Site Region in Plants

11.13 Base Composition Pattern of the Poly(A) Site Region in Animals

11.14 Comparison of Poly(A) Site Region Base Composition Patterns in Plants and Animals

11.15 Common U-A-U-A-U Base Abundance Pattern in the Poly(A) Site Region in Fungi, Plants, and Animals

11.16 Difference between the Most Frequent Motifs and Seqlogo-Showed Most Frequent Bases

11.17 RNA Structure of the Poly(A) Site Region

11.18 Low Conservation in the Overall Nucleotide Sequence of the Poly(A) Site Region

11.19 Poly(A) Site Region Stability and Somatic Genome Variation

11.20 Concluding Remarks

Acknowledgments

References

Chapter 12: Insulin Signaling Pathways in Humans and Plants

12.1 Introduction

12.2 Ranking of the Insulin Signaling Pathway and its Key Proteins

12.3 Diseases Caused by Somatic Mutations of the PI3K, PTEN, and AKT Proteins in the Insulin Signaling Pathway

12.4 Plant Insulin and Medical Use

12.5 Role of the Insulin Signaling Pathway in Regulating Plant Growth

12.6 Concluding Remarks

References

Chapter 13: Developmental Variation in the Nuclear Genome Primary Sequence

13.1 Introduction

13.2 Genetic Mutation, DNA Damage and Protection, and Gene Conversion in Somatic Cells

13.3 Programmed Large-Scale Variation in Primary DNA Sequences in Somatic Nuclear Genome

13.4 Generation of Antibody Genes in Animals through Somatic Genome Variation

13.5 Developmental Variation in Primary DNA Sequences in the Somatic Cells of Plants

13.6 Heritability and Stability of Developmentally Induced Variation in the Somatic Nuclear Genome in Plants

13.7 Concluding Remarks

References

Chapter 14: Ploidy Variation of the Nuclear, Chloroplast, and Mitochondrial Genomes in Somatic Cells

14.1 Introduction

14.2 Nuclear Genome in Somatic Cells

14.3 Plastid Genome Variation in Somatic Cells

14.4 Mitochondrial Genome in Somatic Cells

14.5 Organelle Genomes in Somatic Hybrids

14.6 Effects of Nuclear Genome Ploidy on Organelle Genomes

14.7 Concluding Remarks

Acknowledgments

References

Chapter 15: Molecular Mechanisms of Somatic Genome Variation

15.1 Introduction

15.2 Mutation of Genes Involved in the Cell Cycle, Cell Division, or Centromere Function

15.3 DNA Damage

15.4 Variation in Induction and Activity of Radical-Scavenging Enzymes

15.5 DNA Cytosine Deaminases

15.6 Variation in Protective Roles of Pigments against Oxidative Damage

15.7 RNA-Templated DNA Repair

15.8 Errors in DNA Repair

15.9 RNA-Mediated Somatic Genome Rearrangement

15.10 Repetitive DNA Instability

15.11 Extracellular DNA

15.12 DNATransposition

15.13 Somatic Crossover and Gene Conversion

15.14 Molecular Heterosis

15.15 Genome Damage Induced by Endoplasmic Reticulum Stress

15.16 Telomere Degeneration

15.17 Concluding Remarks

References

Chapter 16: Hypotheses for Interpreting Somatic Genome Variation

16.1 Introduction

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

16.3 Developmental Age and Genomic Network of Reproductive Cells

16.4 Genome Generation Cycle of Species

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

16.6 Costs and Benefits of Somatic Genome Variation

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

16.8 Sources of Genetic Variation from in Vitro Culture Propagation

16.9 Hypothesis that Heterosis Is Created by Somatic Genome Variation

16.10 Genome Stability through Structural Similarity and Sequence Dissimilarity

16.11 Hypothesis Interpreting the Maternal Transmission of Organelles

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

16.13 Concluding Remarks

References

Chapter 17: Impacts of Somatic Genome Variation on Genetic Theories and Breeding Concepts, and the Distinction between Mendelian Genetic Variation, Somagenetic Variation, and Epigenetic Variation

17.1 Introduction

17.2 The Term ‘Somatic Genome’

17.3 Mendelian Genetic Variation, Epigenetic Variation, and Somagenetic Variation

17.4 What Is a Gene?

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

17.6 The Weismann Barrier Hypothesis and the Need for Revision

17.7 Implications for Species Evolution

17.8 Concluding Remarks

References

Chapter 18: Somatic Genome Variation: What it is and What it Means for Agriculture and Human Health

18.1 Introduction

18.2 Natural Attributes of Somatic Genome Variation

18.3 Implications of Somatic Genome Variation for Human and Animal Health

18.4 Implications of Somatic Genome Variation for Agriculture

18.5 Concluding Remarks

Acknowledgments

References

Index

End User License Agreement

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Guide

Cover

Table of Contents

Preface and Introduction

Part I: Somatic Genome Variation in Animals and Humans

Begin Reading

List of Tables

Chapter 1: Polyploidy in Animal Development and Disease

Table 1.1 Polyploidization achieved by varying mechanisms across animal species.

Chapter 5: Environmentally Induced Genome Instability and its Inheritance

Table 5.1 Enzymes involved in DNA methylation.

Table 5.2 Stress and histone modifications.

Chapter 9: Mitotic Genome Variations in Yeast and Other Fungi

Table 9.1 Description of the genes encoding subunits of fungi DNA polymerase complexes and their orthologs in human cells.

Table 9.2 Fungal genes encoding proteins involved in genome maintenance that influence normal or disturbed replication and their human orthologs.

Table 9.3 Effect of translesion synthesis carried out by various DNA polymerases in

S. cerevisiae

cells.

Chapter 10: General Genome Biology 10: Genome Variation in Archaeans, Bacteria, and Asexually Reproducing Eukaryotes

Table 10.1 Correlation between chromosome size and chromosome C+G content in archaeans, gram-positive bacteria, and gram-negative bacteria.

Chapter 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

Table 11.1 Most-frequent hexanucleotide motifs within 50 nucleotides upstream of poly(A) tail starting positions in each species.

Table 11.2 Base abundance values at peak locations of the upstream A-rich region and upstream U-rich region compared between plants and animals.

Somatic Genome Variation in Animals, Plants, and Microorganisms

Edited by Xiu-Qing Li

Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada

This edition first published 2017 © 2017 John Wiley & Sons, Inc.

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List of Contributors

Jennifer L. Bandura

Biology Department

Roanoke College

Salem

USA

Benoit Bizimungu

Fredericton Research and Development Centre

Agriculture and Agri-Food Canada

Fredericton

New Brunswick

Canada

John R. Bracht

Department of Biology

American University

Washington, DC

USA

Normand Brisson

Department of Biochemistry

Université de Montréal

Montréal

Canada

Gregory G. Brown

Department of Biology

McGill University

Montreal

Canada

Christopher A. Cullis

Department of Biology

Case Western Reserve University

Cleveland

USA

Donglei Du

Quantitative Methods Research Group

Faculty of Business Administration

University of New Brunswick

Fredericton

Canada

Silvia Garagna

Laboratorio di Biologia dello Sviluppo

Dipartimento di Biologia e Biotecnologie

Università degli Studi di Pavia

Pavia

Italy

Andrey Golubov

Department of Biological Sciences

University of Lethbridge

Lethbridge

Canada

Étienne Lepage

Department of Biochemistry

Université de Montréal

Montréal

Canada

Xiu-Qing Li

Fredericton Research and Development Centre

Agriculture and Agri-Food Canada

Fredericton

New Brunswick

Canada

Paola Rebuzzini

Laboratorio di Biologia dello Sviluppo

Dipartimento di Biologia e Biotecnologie

Università degli Studi di Pavia

Pavia

Italy

Carlo Alberto Redi

Laboratorio di Biologia dello Sviluppo

Dipartimento di Biologia e Biotecnologie

Università degli Studi di Pavia

Pavia

Italy

Huaijun Si

Gansu Provincial Key Laboratory of Aridland Crop Science

Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement

College of Life Science and Technology

Gansu Agricultural University

Lanzhou

People's Republic of China

Adrianna Skoneczna

Institute of Biochemistry and Biophysics Polish Academy of Sciences

Laboratory of Mutagenesis and DNA Repair

Warsaw

Poland

Marek Skoneczny

Institute of Biochemistry and Biophysics Polish Academy of Sciences

Department of Genetics

Warsaw

Poland

Jeramiah J. Smith

Department of Biology

University of Kentucky

Kentucky

USA

Samuel Tremblay-Belzile

Department of Biochemistry

Université de Montréal

Montréal

Canada

Sébastien Truche

Department of Biochemistry

Université de Montréal

Montréal

Canada

Tim Xing

Department of Biology

Carleton University

Ottawa

Canada

Éric Zampini

Department of Biochemistry

Université de Montréal

Montréal

Canada

Guodong Zhang

Gansu Provincial Key Laboratory of Aridland Crop Science

Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement

College of Life Science and Technology

Gansu Agricultural University

Lanzhou

People's Republic of China

Norman Zielke

Genome-Scale Biology Research Program

Institute of Biomedicine

University of Helsinki

Helsinki

Finland

Maurizio Zuccotti

Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali (SBIBIT)

Università degli Studi di Parma

Parma

Italy

Preface and Introduction

The success of genetic analysis and breeding using Mendel's laws, Johannsen's concepts of genotype and phenotype, Weismann's germ-plasm continuity hypothesis, Morgan's linear arrangement of genes on chromosomes, and Muller's mutation theory leads to a belief—all genes are given by parents and stay the same except for having mutation occasionally caused by external mutagens, somatic cells have no contribution to inheritance, the gene transcript abundance is purely determined by the promoter activity and RNA stability, and clones are genetically identical.

However, as shown in the present book, the somatic genome (the sum total of genetic materials in the cytoplasm and somatic nucleus) actually has environmental and developmental variations; for example: (1) many antibody genes are somatically produced; (2) some ciliate somatic genomes are generated using RNA templates and are therefore phenotypes of the germline genomes but are also the genotypes for many other traits; (3) gene transcription and some endogenous enzymes can induce mutation; (4) certain foods and drinks affect DNA stability and tumor growth; (5) the DNA fingerprint of an animal or plant has certain variations among somatic tissues; (6) various somagenetic and epigenetic variations are transgenerational, and some DNA is translocatable among cells; (7) some genes and repetitive DNA have copy number variation; (8) the chloroplast and mitochondrial genomes vary in ploidy and DNA amount; (9) some DNA sequences are functional through protein binding or DNA-fragment release; (10) DNA damage is sometimes not repaired; (11) clones are genetically mosaic to a certain degree; and (12) the average ploidy level varies among tissues.

This book attempts to assemble the evidence of somatic genome variation in microorganisms, plants, animals, and humans, update various basic concepts in genetics and breeding, determine the implications of somatic genome variation for human health and agriculture, and propose an updated synthesis of inheritance.

Acknowledgments

This book represents the cumulative work of 24 authors from 14 research institutes/universities in six countries. I wish to express my gratitude to all authors who have contributed manuscripts to this book. I thank my Research Centre and my family for their continued support. I would like to extend my very special thanks to the commissioning editor, Mr Justin Jeffryes (the Editorial Director, Natural Sciences, The Americas, at Wiley), Rebecca Ralf, Managing Editor of Life Sciences Books, Ms Divya Narayanan, the primary contact, Ms Bhargavi Natarajan, the former primary contact, Kavitha Chandrasekar, the production editor, Mrs Julie Musk, the copyeditor, and the entire production team at Wiley for their support and high professional standards.

Xiu-Qing Li

About the Editor

Dr Xiu-Qing Li has been a Research Scientist of Molecular Genetics at Agriculture and Agri-Food Canada, Government of Canada (the Fredericton Research and Development Centre, Fredericton, New Brunswick, Canada) since 1997, and an adjunct professor at the University of New Brunswick since 1998. Dr Li received his degree of Docteur d'Etat of France in natural science from Université de Paris-Sud (1987), was an associate professor of biotechnology at Peking University (1987–1993), Invited Professor of Genetics (Université de Paris-Sud, 1988), Research Scientist of Molecular Genetics (Chargée de recherche, level II) at the Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette, France (1987), Visiting Professor at Purdue University (1991–1992), and researcher at McGill University (1992–1997). Dr. Li is an Academic Editor of PloS ONE, co-editor of the book Somatic Genome Manipulation (Li et al. eds, Springer, 2015), on the editorial boards of several other journals, and serves as the Communication Director of the Canadian Association of Plant Biotechnology. He is the organizer and chair for the annual Somatic Genome Workshops (San Diego, since 2010) and a co-organizer of the Genome Features and Chromosome Functionality Workshop (since 2016) at the International Plant and Animal Genome Conferences. Dr. Li has extensive research experience and numerous publications on genetics, genomics, RNA polyadenylation, plant somatic genome, plant genetic engineering, plant cell biology, somaclonal variation, chloroplasts, mitochondria, plant male sterility, plant carbohydrate metabolism, potato genetic improvement, bioinformatic analysis, and genome evolution.

Part ISomatic Genome Variation in Animals and Humans

Chapter 1Polyploidy in Animal Development and Disease

Jennifer L. Bandura1 and Norman Zielke2*

1Biology Department, Roanoke College, Salem, USA

2Genome-Scale Biology Research Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland

* Corresponding author: [email protected] Bandura J.L. and Zielke N. (2017) Polyploidy in animal development and disease. In: Li X.-Q., editor. Somatic Genome Variation in Animals, Plants, and Microorganisms: Wiley-Blackwell, Hoboken, NJ, Ch. 1, pp. 3-44.

Abstract