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Index
Cover image
Title page
Table of Contents
Copyright
Contributors
Preface
Chapter One: Plastid Autonomy vs Nuclear Control Over Plastid Function
Abstract
1 Introduction: Endosymbiosis and the Genomic Remnants of Cyanobacteria in Archaeplastida
2 Cyanobacterial Genes in Two Genetic Compartments
3 Plastid Genomes: Coding Capacity and Functional Diversity
4 Role of Genetic Autonomy in Endosymbiosis
5 Kleptoplasty and Genetic Semiautonomy of (Stolen) Plastids
6 Plastid Autonomy and the Evolution of Land Plants
7 Outlook
Acknowledgements
Chapter Two: Lost in the Light: Plastid Genome Evolution in Nonphotosynthetic Algae
Abstract
1 Introduction
2 And Then There Was Light
3 Burning Out: The Evolutionary Loss of Photosynthesis
4 Genetic Ball and Chain: Plastomes in Colourless Algae
5 Adiós ptDNA: The Outright Loss of a Plastome
6 Nonphotosynthetic ptDNA: Not so Small After All
7 Concluding Thoughts
Acknowledgements
Chapter Three: Plastid Genomes in the Myzozoa
Abstract
1 Introduction
2 The Myzozoa
3 The Origin of Myzozoan Plastids
4 Diversity of Plastids in the Myzozoa
5 The Plastomes of Myzozoans
6 Gene Transfer in Myzozoans
7 Conclusions and Future Directions
Acknowledgements
Chapter Four: Comparative Plastid Genomics of Glaucophytes
Abstract
1 Introduction
2 The Glaucophyta Plastids, Organelles With Ancestral Morphological Traits
3 The Genetic Repertoire of the Blue-Green Plastids
4 Interspecific Comparative Genomics
5 Phylogenomics, the Origin of the Primary Plastids and the Archaeplastida Hypothesis
6 The Known Glaucophyte Groups Represent Lineages of Putative Ancient Divergence
7 Conclusions
Chapter Five: Evolution of the Plastid Genomes in Diatoms
Abstract
1 Introduction
2 Materials and Methods
3 Results
4 Discussion
Acknowledgements
Author Contributions
Chapter Six: Evolution of the Plastid Genome in Green Algae
Abstract
1 Introduction
2 Classification and Phylogeny of Green Algae
3 Plastome Architecture of the Common Ancestor of All Green Algae
4 Plastome Evolution in the Chlorophyta
5 Plastome Evolution in Streptophyte Algae
6 Future Directions
Chapter Seven: Evolution of Gymnosperm Plastid Genomes
Abstract
1 Introduction
2 Sequencing the Plastomes of Gymnosperms
3 Plastome Characteristics in Gymnosperms
4 Plastome Rearrangements
5 Evolution of Nucleotide Substitution Rates
6 Plastid Phylogenomics of Gymnosperms
7 Conclusions and Future Directions
Acknowledgments
Chapter Eight: Aberration or Analogy? The Atypical Plastomes of Geraniaceae
Abstract
1 Introduction
2 The Great and the Small
3 Change or Stay the Same
4 Keeping Up With the Rate Race: Acceleration and Coevolution
5 Staying in Sync: Hybrid Harmony or Dissonance
6 Aberration or Analogy?
Acknowledgements
Chapter Nine: Structural Diversity Among Plastid Genomes of Land Plants
Abstract
1 Introduction
2 Typical Structure of a Land Plant Plastome
3 Conserved Plastomes and Inference of Ancestral Structures
4 Structural Diversity of the Plastome Among Plants
5 Functional Effect of Structural Change
6 What Is Left in Plastome Structural Research?
Acknowledgements
Chapter Ten: Plastome Phylogenetics: 30 Years of Inferences Into Plant Evolution
Abstract
1 Introduction
2 The Plastid Genome and Plant Systematics
3 Plastome Phylogeny: State of the Tree
4 Plastome Phylogenetics: Ongoing Challenges
5 Conclusions
Chapter Eleven: Molecular Evolution of Plastid Genomes in Parasitic Flowering Plants
Abstract
1 Introduction
2 Plastome Size Diversity in Heterotrophic Land Plants
3 Reconstructing and Annotating Divergent Plastomes of Heterotrophs
4 Are We Always Dealing With (Pseudo)genes?
5 Evolution of Plastome Structure Under Relaxed Selective Constraints
6 Functional Reduction Along the Transition to a Nonphotosynthetic Lifestyle
7 Evolution of Substitution Rates
8 Models of Plastome Degradation
9 Conclusions and Future Directions
Acknowledgements
Subject Index
Author Index
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