Plant Transposons and Genome Dynamics in Evolution -- Contents -- Contributors -- Foreword -- Introduction -- 1 The Discovery of Transposition -- Introduction -- Studies on Variegation -- Mutable Genes -- McClintock's Studies on Chromosome Breakage -- Recognition that Ds Transposes -- Explaining Mutable Genes -- Molecular Endnote -- References -- 2 A Field Guide to Transposable Elements -- The C-value Paradox -- The Quantity of Transposable Elements Determines Genome Size -- General Classification Scheme for Transposable Elements -- Class II Elements -- Class I: The Non-LTR and LTR Retrotransposons -- Evolutionary Origins of Transposable Elements -- Non-autonomous Transposable Elements -- Transposable Element Demography and Genome Ecology -- Conclusions: Rehabilitation of Transposable Elements -- Acknowledgments -- References -- 3 The Mechanism of Ac/Ds Transposition -- Transposition of Ac/Ds Elements -- The Enigmatic Ac Dosage Effect -- cis and trans Effects on Ac/Ds Transposition -- Molecular Characterization of Transposable Elements -- The Excision and Insertion Reactions -- Formation of Ds from Ac -- Standard versus Alternative Transposition -- Sister Chromatid Transposition -- Reversed-ends Transposition -- How Does Ds Break Chromosomes? -- Alternative Transposition, DNA Methylation, and the Sequence of Transposition Reactions -- Potential Applications of Alternative Transposition -- Perspective -- References -- 4 McClintock and Epigenetics -- Introduction -- Spm-suppressible Alleles -- Spm-dependent Alleles -- Cryptic Spm -- Presetting -- Molecular Machinery of Epigenetic Regulation -- Summary -- References -- 5 Molecular Mechanisms of Transposon Epigenetic Regulation -- Introduction -- Chromatin Remodeling, DNA and Histone Modification -- Replication-Dependent DNA Methylation -- Histone Modification and DNA Methylation.

Enzymatic Loss of DNA and Histone Methylation -- RNA Interference (RNAi) and RNA-Directed DNA Methylation (RdDM) -- RNAi-Guided Histone Modification -- RNA-Dependent DNA Methylation -- Interaction Between RNA-Dependent and Replication-Dependent DNA Methylation -- Functional Consequences of Epigenetic Regulation -- Heterochromatin Reprogramming and Germ Cell Fate -- Reprogramming in the Male Germline -- Reprogramming in the Female Germline -- Transgenerational Inheritance of Transposon Silencing -- Paramutation -- Conclusions -- References -- 6 Transposons in Plant Gene Regulation -- Introduction -- New Regulatory Functions -- TE-Induced Down-Regulation -- Deletions and Rearrangements -- Suppressible Alleles -- TEs and Plant Domestication -- The Dynamic Genome -- References -- 7 Imprinted Gene Expression and the Contribution of Transposable Elements -- Why are Genes Imprinted? -- The Developmental Origin of Endosperm -- Selection for Imprinted Expression -- Principles Derived from the First Imprinted Gene -- Gene Imprinting and Parent-of-Origin Effects on Seed Development -- What Genes are Imprinted? -- Epigenome Dynamics during Seed Development -- Epigenetic Landscape in Vegetative Tissues -- Cytological Observations of Chromatin in Seeds -- Epigenomic Profiling in Seeds -- Mechanisms of Gene Imprinting and the Relation to TEs -- FWA -- MEDEA -- PHERES1 -- TEs and Allele-Specific Imprinting -- Insights from Whole Genome Studies -- Outstanding Questions -- References -- 8 Transposons and Gene Creation -- Introduction -- Capture of Gene Fragments by TEs and Formation of Chimeric Genes -- Capture of Gene Fragments and Formation of Chimeric Genes by DNA Elements -- Capture of Gene Fragments and Formation of Chimeric Genes by RNA Elements -- Co-Option of a TE Gene by the Host -- Fusion of TE and Host Genes.

Alterations of Host Gene Sequences by TE Excisions -- Alterations of Host Coding Sequences by TE Insertions -- Acquisition by Host Genes of New Regulatory Sequences from TEs -- Interaction of TEs with Target Gene mRNA Splicing and Structure -- Reshuffling of Host Sequences by Alternative Transpositions -- Conclusion -- References -- 9 Transposons in Plant Speciation -- Introduction -- Genetic Models of Speciation -- Speciation - a Gradual or a Rapid Process? -- Speciation Through Accumulation of Mutations -- DNA Cut-and-Paste TEs and Speciation -- Copy-and-Paste TEs and Speciation -- TE-Mediated Speciation - a Likely Scenario? -- Plant Speciation Through Hybridization and Allopolyploidization -- Induction of Transposition upon Hybridization and Polyploidization -- Epigenetic Alteration of TEs upon Hybridization and Polyploidization -- Transcriptional Activation of TEs upon Hybridization and Polyploidization -- Alterations in Small RNAs upon Hybridization and Polyploidization -- A Mechanistic Model for Responses to Genome Shock -- Dysregulation of Gene Expression by Novel Interactions Between Regulatory Factors -- Altered Protein Complexes -- Why TEs Become Activated when Cellular Processes are Dysregulated -- Conclusions -- Acknowledgments -- References -- 10 Transposons, Genomic Shock, and Genome Evolution -- How Transposons Came to be Called "Selfish" DNA -- The "Selfish DNA" Label Stuck to Transposons -- Transposons Coevolved with Eukarotic Genomes -- Sequence Duplication: The Real Innovation -- The Facilitator: Epigenetic Control of Homologous Recombination -- Epigenetic Mechanisms, Duplication and Genome Evolution -- Plant Genome Organization: Gene Islands in a Sea of Repetitive DNA -- Transposon Neighborhoods and Insertion Site Selection -- Genome Evolution: Colinearity and Its Erosion.

Genome Contraction and Divergence of Intergenic Sequences -- Transposases Sculpt Genomes -- Small Regulatory RNAs from Transposons -- Genome Shocks -- Genome Evolvability -- References -- Index -- Supplemental Images.