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E-raamat: Somatic Genome Variation in Animals, Plants, and Microorganisms: in Animals, Plants, and Microorganisms [Wiley Online]

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  • Formaat: 448 pages
  • Ilmumisaeg: 20-Jun-2017
  • Kirjastus: Wiley-Blackwell
  • ISBN-10: 1118647114
  • ISBN-13: 9781118647110
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Somatic Genome Variation in Animals, Plants, and Microorganisms: in Animals, Plants, and MicroorganismsSuurem pilt
  • Formaat: 448 pages
  • Ilmumisaeg: 20-Jun-2017
  • Kirjastus: Wiley-Blackwell
  • ISBN-10: 1118647114
  • ISBN-13: 9781118647110
Teised raamatud teemal:
Wiley Online e-raamatudRohkem infot Wiley Online kohta
Raamatu kodulehekülg: https://onlinelibrary.wiley.com/doi/book/10.1002/9781118647110

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.

List of Contributors xv
Preface and Introduction xix
Acknowledgments xxi
About the Editor xxiii
Part I Somatic Genome Variation in Animals and Humans 1(74)
1 Polyploidy in Animal Development and Disease
3(42)
Jennifer L. Bandura
Norman Zielke
1.1 Introduction
3(1)
1.2 Mechanisms Inducing Somatic Polyploidy
4(4)
1.2.1 Cell Fusion
4(1)
1.2.2 Acytokinetic Mitosis
4(1)
1.2.3 Endomitosis
5(1)
1.2.4 Endoreplication
5(2)
1.2.5 Gene Amplification
7(1)
1.2.6 Ploidy Reversal
7(1)
1.3 The Core Cell Cycle Machinery
8(1)
1.4 Genomic Organization of Polyploid Cells
9(1)
1.5 Endoreplication: An Effective Tool for Post-Mitotic Growth and Tissue Regeneration
10(1)
1.6 Initiation of Endoreplication in Drosophila
11(4)
1.6.1 Endocycle Entry in Ovarian Follicle Cells
11(2)
1.6.2 Signaling Pathways Regulating Endocycle Entry in Follicle Cells
13(1)
1.6.3 Endocycle Entry in Other Tissues
14(1)
1.7 Mechanisms of Endocycle Oscillations in Drosophila
15(2)
1.7.1 An Autonomous Oscillator Drives Endocycling in the Salivary Gland
15(2)
1.7.2 Alternative Modes of Endoreplication
17(1)
1.8 Gene Amplification in Drosophila Follicle Cells
17(2)
1.8.1 Molecular Mechanism of Gene Amplification
17(2)
1.8.2 The Endocycle-to-Amplification Switch
19(1)
1.9 Endocycle Entry in the Trophoblast Lineage
19(3)
1.10 Mechanisms of Endocycle Oscillations in Trophoblast Giant Cells
22(1)
1.11 Cardiomyocytes
23(2)
1.11.1 Upstream Control of Cardiomyocyte Polyploidization
23(1)
1.11.2 Mechanisms of Cardiomyocyte Polyploidization
24(1)
1.11.3 Polyploidization as a Response to Tissue Damage
25(1)
1.12 Hepatocytes
25(3)
1.12.1 Mechanisms of Hepatocyte Polyploidization
25(1)
1.12.2 The Ploidy Conveyor Model
26(1)
1.12.3 Liver Regeneration
26(2)
1.13 Megakaryocytes
28(2)
1.13.1 Mechanisms of MKC Polyploidization
28(2)
1.14 Concluding Remarks
30(1)
Acknowledgments
31(1)
References
31(14)
2 Large-Scale Programmed Genome Rearrangements in Vertebrates
45(10)
Jeramiah J. Smith
2.1 Introduction
45(1)
2.1 Hagfish
46(2)
2.2.1 Content of Eliminated DNA
47(1)
2.2.2 Results and Mechanisms of Deletion
47(1)
2.3 Sea Lamprey
48(1)
2.3.1 Content of Eliminated DNA
48(1)
2.3.2 Results and Mechanisms of Deletion
48(1)
2.4 Zebra Finch
48(1)
2.4.1 Mechanisms of Deletion
49(1)
2.4.2 Content of Eliminated DNA
49(1)
2.5 Emerging Themes and Directions
49(2)
2.5.1 The Biological Function of PGR
49(1)
2.5.2 Mechanisms of Deletion
50(1)
2.5.3 Other Vertebrates?
51(1)
References
51(4)
3 Chromosome Instability in Stem Cells
55(20)
Paola Rebuzzini
Maurizio Zuccotti
Carlo Alberto Redi
Silvia Garagna
3.1 Introduction
55(1)
3.2 Pluripotent Stem Cells
56(2)
3.2.1 Primate Embryonic Stem Cells
56(1)
3.2.2 Mouse Embryonic Stem Cells
57(1)
3.2.3 Parthenogenetic Embryonic Stem Cells
57(1)
3.2.4 Induced Pluripotent Stem Cells
58(1)
3.3 Somatic Stem Cells
58(1)
3.3.1 Mesenchymal Stem Cells
58(1)
3.3.2 Neural Stem Cells
59(1)
3.4 Mechanisms of Chromosomal Instability
59(4)
3.4.1 Dysfunction in the Spindle Assembly Checkpoints
60(1)
3.4.2 Defects of Microtubule Attachment to the Kinetochore
60(1)
3.4.3 Supernumerary Centrosomes
61(1)
3.4.4 Sister Chromatids Cohesion
62(1)
3.5 Mechanisms of Chromosomal Instability in Stem Cells
63(1)
References
63(12)
Part II Somatic Genome Variation in Plants 75(90)
4 Mechanisms of Induced Inheritable Genome Variation in Flax
77(14)
Christopher A. Cullis
4.1 Introduction
77(2)
4.2 Restructuring the Flax Genome
79(1)
4.3 Specific Genomic Changes
80(3)
4.4 What Happens When Plastic Plants Respond to Environmental Stresses?
83(1)
4.5 When Do the Genomic Changes Occur and Are they Adaptive?
83(1)
4.6 Is this Genomic Response of Flax Unique?
84(3)
4.7 Concluding Remarks
87(1)
Acknowledgments
87(1)
References
87(4)
5 Environmentally Induced Genome Instability and its Inheritance
91(12)
Andrey Golubov
5.1 Introduction
91(1)
5.2 Stress and its Effects on Genomes
92(4)
5.2.1 Genetic Changes
92(1)
5.2.2 DNA Repair
92(1)
5.2.3 Epigenetic Changes
93(1)
5.2.3.1 DNA Methylation
93(1)
5.2.3.2 Histone Modifications
95(1)
5.2.4 The Link between Genetic and Epigenetic Changes
95(1)
5.3 Transgenerational Inheritance
96(1)
5.4 Concluding Remarks
97(1)
Acknowledgments
97(1)
References
97(6)
6 The Mitochondria! Genome, Genomic Shifting, and Genomic Conflict
103(16)
Gregory G. Brown
6.1 Introduction
103(2)
6.2 Heteroplasmy and Sublimons
105(3)
6.3 Cytoplasmic Male Sterility (CMS) in Plants
108(1)
6.4 Mitochondrial Sublimons and CMS
109(2)
6.5 Restorer Gene Evolution: Somatic Genetic Changes Drive Nuclear Gene Diversity?
111(1)
6.6 Concluding Remarks
112(1)
References
113(6)
7 Plastid Genome Stability and Repair
119(46)
Eric Zampini
Sebastien Truche
Etienne Lepage
Samuel Tremblay-Belzile
Normand Brisson
7.1 Introduction
120(1)
7.2 Characteristics of the Plastid Genome
121(3)
7.2.1 General Composition of the Plastid Genome
121(2)
7.2.2 The Structure of the Plastid Genome
123(1)
7.3 Replication of Plastid DNA
124(6)
7.3.1 Plastid DNA Content during Development
124(1)
7.3.2 Plastid DNA Replication Machinery
125(1)
7.3.3 Replication Mechanisms
126(3)
7.3.4 Origins of Replication
129(1)
7.3.5 Nucleus and Plastid Coordination during DNA Replication
130(1)
7.4 Transcription in the Plastid
130(1)
7.5 The Influence of Replication and Transcription on Plastid Genome Stability
131(2)
7.6 Plastid Genome Stability and DNA Repair
133(12)
7.6.1 Oxidative Stress, Photo-Adaptation, and ROS Detoxification
133(5)
7.6.2 UV-Induced DNA Damage
138(3)
7.6.3 Recombination and DNA Double-Strand Break Repair
141(4)
7.7 Outcomes of DNA Rearrangements
145(2)
7.8 Concluding Remarks
147(1)
References
148(17)
Part III Somatic Genome Variation in Microorganisms 165(86)
8 RNA-Mediated Somatic Genome Rearrangement in Ciliates
167(32)
John R. Bracht
8.1 Introduction
168(1)
8.2 Ciliates: Ubiquitous Eukaryotic Microorganisms with a Long Scientific History
168(2)
8.3 Two's Company: Nuclear Dimorphism in Ciliates
170(1)
8.4 Paramecium: Non-Mendelian Inheritance Comes to Light
171(2)
8.5 Tetrahymena and the Origin of the scanRNA Model
173(2)
8.6 Small RNAs in Stylonychia and Oxytricha
175(1)
8.7 Long Noncoding RNA Templates in Genome Rearrangement
176(1)
8.8 Long Noncoding RNA: An Interface for Short Noncoding RNA
177(2)
8.9 Short RNA-Mediated Heterochromatin Formation and DNA Elimination
179(3)
8.10 Transposable Elements and the Origins of Genome Rearrangements
182(3)
8.11 Transposons, Phase Variation, and Programmed Genome Engineering in Bacteria
185(1)
8.12 Transposases, Noncoding RNA, and Chromatin Modifications in VDJ Recombination of Vertebrates
186(1)
8.13 Concluding Remarks: Ubiquitous Genome Variation, Transposons, and Noncoding RNA
187(1)
Acknowledgments
187(1)
References
187(12)
9 Mitotic Genome Variations in Yeast and Other Fungi
199(52)
Adrianna Skoneczna
Marek Skoneczny
9.1 Introduction
199(1)
9.2 The Replication Process as a Possible Source of Genome Instability
200(19)
9.2.1 DNA Polymerases as Guardians of Genome Maintenance
201(4)
9.2.2 dNTP Cellular Level and their Pool Bias Contribute to Genome Stability
205(13)
9.2.3 Mismatch Repair (MMR) and Ribonucleotide Excision Repair (RER) Are Used to Clean-up after Replication
218(1)
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(10)
9.3.1 Sumoylated PCNA-, Srs2-, and Replicative Polymerase-dependent DNA Synthesis on Damaged Template
221(2)
9.3.2 Ubiquitinated PCNA- and Specialized Pol-Dependent Translesion Synthesis
223(2)
9.3.3 The Polyubiquitinated PCNA- and RadS-Dependent Damage Avoidance Pathway
225(1)
9.3.4 The Alternative PCNA-, RPA-, and 5'-Junction-Dependent Pathway Involved in Gap Filling and Telomere Maintenance
226(1)
9.3.5 Crosstalk between RFC Complexes Adapts Cellular Response to Different Stresses Arising from Genome Perturbations
226(1)
9.3.6 Break-Induced Replication (BIR) Is a Vastly Inaccurate Repair Pathway
227(2)
9.4 Ploidy Maintenance and Chromosome Integrity Mechanisms
229(5)
9.4.1 Processes that Affect Aneuploidy in Yeasts
230(1)
9.4.2 Ploidy Changes in Yeasts
231(1)
9.4.3 Possible Mechanism of Ploidy Change in Yeast
232(2)
9.5 Concluding Remarks
234(1)
References
235(16)
Part IV General Genome Biology 251(154)
10 Genome Variation in Archaeans, Bacteria, and Asexually Reproducing Eukaryotes
253(14)
Xiu-Qing Li
10.1 Introduction
254(1)
10.2 Chromosome Number in Prokaryote Species
254(1)
10.3 Genome Size Variation in Archaeans and Bacteria
255(1)
10.4 Archaeal and Bacterial Genome Size Distribution
256(1)
10.5 Genomic GC Content in Archaeans, Bacteria, Fungi, Protists, Plants, and Animals
257(2)
10.6 Correlation between GC Content and Genome or Chromosome Size
259(1)
10.7 Genome Size and GC-Content Variation in Primarily Asexually Reproducing Fungi
260(3)
10.8 Variation of Gene Direction
263(1)
10.9 Concluding Remarks
263(1)
Acknowledgments
264(1)
References
264(3)
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(24)
Xiu-Qing Li
Donglei Du
11.1 General Introduction to Gene Number, Direction, and RNA Polyadenylation
268(1)
11.2 Base Selection at the Poly(A) Tail Starting Position
269(2)
11.3 Most Frequent Upstream Motifs in Microorganisms, Plants, and Animals
271(2)
11.4 Motif Frequencies in the Whole Genome
273(1)
11.5 The Top 20 Hexamer Motifs in the Poly(A) Site Region in Humans
273(1)
11.6 Polyadenylation Signal Motif Distribution
273(2)
11.7 Alternative Polyadenylation
275(1)
11.8 Base Composition of 3'UTR in Plants and Animals
276(1)
11.9 Base Composition Comparison between 3'UTR and Whole Genome
276(1)
11.10 Base Composition of 3'COR in Plants and Animals
277(1)
11.11 Base Composition Pattern of the Poly(A) Site Region in Protists
278(2)
11.12 Base Composition Pattern of the Poly(A) Site Region in Plants
280(1)
11.13 Base Composition Pattern of the Poly(A) Site Region in Animals
280(1)
11.14 Comparison of Poly(A) Site Region Base Composition Patterns in Plants and Animals
280(4)
11.15 Common U-A-U-A-U Base Abundance Pattern in the Poly(A) Site Region in Fungi, Plants, and Animals
284(1)
11.16 Difference between the Most Frequent Motifs and Seqlogo-Showed Most Frequent Bases
284(2)
11.17 RNA Structure of the Poly(A) Site Region
286(1)
11.18 Low Conservation in the Overall Nucleotide Sequence of the Poly(A) Site Region
286(1)
11.19 Poly(A) Site Region Stability and Somatic Genome Variation
286(1)
11.20 Concluding Remarks
287(1)
Acknowledgments
288(1)
References
288(3)
12 Insulin Signaling Pathways in Humans and Plants
291(8)
Xiu-Qing Li
Tim Xing
12.1 Introduction
291(2)
12.2 Ranking of the Insulin Signaling Pathway and its Key Proteins
293(1)
12.3 Diseases Caused by Somatic Mutations of the PI3K, PTEN, and AKT Proteins in the Insulin Signaling Pathway
293(2)
12.4 Plant Insulin and Medical Use
295(1)
12.5 Role of the Insulin Signaling Pathway in Regulating Plant Growth
295(1)
12.6 Concluding Remarks
295(1)
References
296(3)
13 Developmental Variation in the Nuclear Genome Primary Sequence
299(10)
Xiu-Qing Li
13.1 Introduction
299(1)
13.2 Genetic Mutation, DNA Damage and Protection, and Gene Conversion in Somatic Cells
300(2)
13.3 Programmed Large-Scale Variation in Primary DNA Sequences in Somatic Nuclear Genome
302(1)
13.4 Generation of Antibody Genes in Animals through Somatic Genome Variation
303(1)
13.5 Developmental Variation in Primary DNA Sequences in the Somatic Cells of Plants
303(1)
13.6 Heritability and Stability of Developmentally Induced Variation in the Somatic Nuclear Genome in Plants
303(1)
13.7 Concluding Remarks
304(1)
References
305(4)
14 Ploidy Variation of the Nuclear, Chloroplast, and Mitochondria! Genomes in Somatic Cells
309(28)
Xiu-Qing Li
Benoit Bizimungu
Guodong Zhang
Huaijun Si
14.1 Introduction
310(1)
14.2 Nuclear Genome in Somatic Cells
311(6)
14.2.1 Ploidy Variation of the Individual or Species in Plants and Animals
311(1)
14.2.2 Effects of Species Ploidy Variation on the Growth of Animals and Plants
312(1)
14.2.3 Ploidy of Bacteria
313(1)
14.2.4 Endopolyploidy in Animal and Plant Somatic Cells
313(2)
14.2.5 Somatic Cell Haploidization
315(1)
14.2.6 Aneuploid Cells in Plant Somatic Tissues
315(1)
14.2.7 Aneuploid Cells in Cancerous Masses
316(1)
14.2.8 Nuclear B Chromosomes in Somatic Cells
316(1)
14.3 Plastid Genome Variation in Somatic Cells
317(3)
14.3.1 Types of Plastids
317(1)
14.3.2 Plastid Genome and its Size in Somatic Cells
317(1)
14.3.3 Recombination among Repeated Sequences in the Plastid Genome
318(1)
14.3.4 Integrity of the Organelle Genome in Green Leaves under Light
318(1)
14.3.5 Plastid Genome Ploidy or Copy Number Variation in Somatic Cells
319(1)
14.4 Mitochondrial Genome in Somatic Cells
320(4)
14.4.1 Mitochondrial Genome and its Size
320(1)
14.4.2 Recombination among Repeated Sequences and Subgenomic Molecules in Mitochondria
321(1)
14.4.3 Mitochondrial Subgenome Copy Number Variation in Somatic Cells
322(1)
14.4.4 Nuclear and Tissue-Specific Regulation of Mitochondrial Gene Expression
322(1)
14.4.5 Stoichiometric Variation and Effects on Mitochondrial Subgenomic Molecules
323(1)
14.5 Organelle Genomes in Somatic Hybrids
324(1)
14.6 Effects of Nuclear Genome Ploidy on Organelle Genomes
325(1)
14.7 Concluding Remarks
326(1)
Acknowledgments
326(1)
References
326(11)
15 Molecular Mechanisms of Somatic Genome Variation
337(14)
Xiu-Qing Li
15.1 Introduction
338(1)
15.2 Mutation of Genes Involved in the Cell Cycle, Cell Division, or Centromere Function
338(1)
15.3 DNA Damage
338(1)
15.4 Variation in Induction and Activity of Radical-Scavenging Enzymes
339(1)
15.5 DNA Cytosine Deaminases
340(1)
15.6 Variation in Protective Roles of Pigments against Oxidative Damage
340(1)
15.7 RNA-Templated DNA Repair
341(1)
15.8 Errors in DNA Repair
341(1)
15.9 RNA-Mediated Somatic Genome Rearrangement
342(1)
15.10 Repetitive DNA Instability
342(1)
15.11 Extracellular DNA
343(1)
15.12 DNA Transposition
343(1)
15.13 Somatic Crossover and Gene Conversion
343(1)
15.14 Molecular Heterosis
344(1)
15.15 Genome Damage Induced by Endoplasmic Reticulum Stress
344(1)
15.16 Telomere Degeneration
344(1)
15.17 Concluding Remarks
344(1)
References
345(6)
16 Hypotheses for Interpreting Somatic Genome Variation
351(12)
Xiu-Qing Li
16.1 Introduction
352(1)
16.2 Cell-Specific Accumulation of Somatic Genome Variation in Somatic Cells
352(1)
16.3 Developmental Age and Genomic Network of Reproductive Cells
353(1)
16.4 Genome Generation Cycle of Species
353(1)
16.5 Somatic Genome Variation and Tissue-Specific Requirements during Growth or Development
354(1)
16.6 Costs and Benefits of Somatic Genome Variation
354(1)
16.7 Hypothesis on the Existence of a Primitive Stage in both Animals and Plants
355(2)
16.8 Sources of Genetic Variation from in Vitro Culture Propagation
357(1)
16.9 Hypothesis that Heterosis Is Created by Somatic Genome Variation
357(1)
16.10 Genome Stability through Structural Similarity and Sequence Dissimilarity
358(1)
16.11 Hypothesis Interpreting the Maternal Transmission of Organelles
358(1)
16.12 Ability of Humans to Deal with Somatic Genome Variation and Diseases
359(1)
16.13 Concluding Remarks
360(1)
References
360(3)
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(14)
Xiu-Qing Li
17.1 Introduction
364(1)
17.2 The Term 'Somatic Genome'
365(1)
17.3 Mendelian Genetic Variation, Epigenetic Variation, and Somagenetic Variation
365(2)
17.4 What Is a Gene?
367(1)
17.5 Breeding Criteria, Genome Cycle, Pure Lines, and Variety Stability
368(2)
17.6 The Weismann Barrier Hypothesis and the Need for Revision
370(1)
17.7 Implications for Species Evolution
370(1)
17.8 Concluding Remarks
371(1)
References
372(5)
18 Somatic Genome Variation: What it is and What it Means for Agriculture and Human Health
377(28)
Xiu-Qing Li
18.1 Introduction
378(1)
18.2 Natural Attributes of Somatic Genome Variation
378(2)
18.3 Implications of Somatic Genome Variation for Human and Animal Health
380(5)
18.3.1 Cellular-Level Variation
380(1)
18.3.2 Ploidy and Chromosome Number Variation of the Whole Organism
380(1)
18.3.3 Endoploidy Variation
381(1)
18.3.4 DNA Cytosine Deaminases, Somatic Mutation, Immunoglobulin Diversity, and Tumors
381(3)
18.3.5 Mitochondrial Genome Sequence or DNA Amount Variation
384(1)
18.3.6 Nuclear or Ooplasmic Transfer-Based Therapy
385(1)
18.3.7 Differential Treatments of Beneficial and Harmful SGVs
385(1)
18.4 Implications of Somatic Genome Variation for Agriculture
385(6)
18.4.1 Cellular-Level Variation
385(1)
18.4.2 Ploidy and Chromosome Number Variation of the Whole Organism
386(1)
18.4.3 Endoploidy Variation
387(1)
18.4.4 Intra- and Interchromosomal Variation
387(1)
18.4.5 Dedifferentiation- and Redifferentiation-Induced Variation
388(1)
18.4.6 DNA Damage, Epigenetics, Gene Mutation, and Bud Mutation
389(1)
18.4.7 Plastid Genome Sequence or DNA Amount Variation
389(1)
18.4.8 Mitochondrial Genome Sequence or DNA Amount Variation
390(1)
18.4.9 DNA Transfer, Organelle Transmission, and Organelle Genome Segregation
390(1)
18.4.10 Intercompartmental Interaction and DNA Exchange
391(1)
18.5 Concluding Remarks
391(1)
Acknowledgments
392(1)
References
392(13)
Index 405
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.
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