Plant Molecular Biology

  1. The Plant Genome: Organization and Dynamics
    1. Nuclear Genome
      1. Chromosome Structure and Organization
        1. Chromosome Number and Size
          1. Karyotype Analysis
            1. Centromeres and Telomeres
              1. Centromere Structure
                1. Telomere Maintenance
                2. Chromosome Banding and Staining
                3. Gene Structure and Organization
                  1. Gene Architecture
                    1. Exons and Introns
                      1. Untranslated Regions
                        1. Regulatory Sequences
                        2. Gene Density and Distribution
                          1. Gene Clusters and Families
                            1. Tandem Gene Arrays
                              1. Dispersed Gene Families
                              2. Pseudogenes
                                1. Formation Mechanisms
                                  1. Evolutionary Significance
                                2. Repetitive DNA Sequences
                                  1. Tandem Repeats
                                    1. Satellite DNA
                                      1. Ribosomal RNA Genes
                                      2. Interspersed Repeats
                                        1. Minisatellites and Microsatellites
                                          1. Structure and Function
                                            1. Genetic Markers
                                          2. Transposable Elements
                                            1. Classification and Mechanisms
                                              1. Class I: Retrotransposons
                                                1. LTR Retrotransposons
                                                  1. Structure and Mechanism
                                                    1. Examples in Plants
                                                    2. Non-LTR Retrotransposons
                                                      1. LINE Elements
                                                        1. SINE Elements
                                                      2. Class II: DNA Transposons
                                                        1. Cut-and-Paste Mechanism
                                                          1. Autonomous Elements
                                                            1. Non-Autonomous Elements
                                                            2. Impact on Genome Evolution
                                                              1. Genome Size Variation
                                                                1. Gene Disruption
                                                                  1. Regulatory Evolution
                                                              2. Organellar Genomes
                                                                1. Chloroplast Genome (Plastome)
                                                                  1. Structure and Organization
                                                                    1. Quadripartite Structure
                                                                      1. Large Single Copy Region
                                                                        1. Small Single Copy Region
                                                                          1. Inverted Repeat Regions
                                                                          2. Gene Content and Function
                                                                            1. Photosynthesis Genes
                                                                              1. Ribosomal Genes
                                                                                1. Transfer RNA Genes
                                                                                2. Inheritance Patterns
                                                                                  1. Maternal Inheritance
                                                                                    1. Biparental Inheritance
                                                                                    2. RNA Editing
                                                                                      1. C-to-U Editing
                                                                                        1. Editing Sites
                                                                                      2. Mitochondrial Genome (Chondriome)
                                                                                        1. Structure and Organization
                                                                                          1. Variable Structure
                                                                                            1. Gene Content
                                                                                            2. Recombination and Rearrangement
                                                                                              1. Repeat-Mediated Recombination
                                                                                                1. Genome Plasticity
                                                                                                2. RNA Editing
                                                                                                  1. Extensive C-to-U Editing
                                                                                                    1. Trans-Splicing
                                                                                                  2. Endosymbiotic Theory and Gene Transfer
                                                                                                    1. Evidence for Endosymbiosis
                                                                                                      1. Phylogenetic Evidence
                                                                                                        1. Biochemical Similarities
                                                                                                        2. Gene Transfer to Nucleus
                                                                                                          1. Mechanisms of Transfer
                                                                                                            1. Functional Relocation
                                                                                                            2. Functional Integration
                                                                                                              1. Protein Import Systems
                                                                                                                1. Coordinated Gene Expression
                                                                                                            3. Epigenetics and Chromatin Regulation
                                                                                                              1. DNA Methylation
                                                                                                                1. Cytosine Methylation Patterns
                                                                                                                  1. CG Methylation
                                                                                                                    1. CHG Methylation
                                                                                                                      1. CHH Methylation
                                                                                                                      2. Methylation Machinery
                                                                                                                        1. DNA Methyltransferases
                                                                                                                          1. Demethylases
                                                                                                                          2. Role in Gene Silencing
                                                                                                                            1. Promoter Methylation
                                                                                                                              1. Transposon Silencing
                                                                                                                            2. Histone Modifications
                                                                                                                              1. Acetylation
                                                                                                                                1. Histone Acetyltransferases
                                                                                                                                  1. Histone Deacetylases
                                                                                                                                    1. Effects on Chromatin Structure
                                                                                                                                    2. Methylation
                                                                                                                                      1. Histone Methyltransferases
                                                                                                                                        1. Histone Demethylases
                                                                                                                                          1. Effects on Gene Expression
                                                                                                                                          2. Phosphorylation
                                                                                                                                            1. Cell Cycle Regulation
                                                                                                                                              1. Stress Response
                                                                                                                                              2. Other Modifications
                                                                                                                                                1. Ubiquitination
                                                                                                                                                  1. SUMOylation
                                                                                                                                                2. Chromatin Remodeling
                                                                                                                                                  1. ATP-Dependent Complexes
                                                                                                                                                    1. SWI/SNF Complexes
                                                                                                                                                      1. ISWI Complexes
                                                                                                                                                      2. Nucleosome Positioning
                                                                                                                                                        1. Chromatin Accessibility
                                                                                                                                                        2. Epigenetic Inheritance
                                                                                                                                                          1. Transgenerational Inheritance
                                                                                                                                                            1. Epigenetic Memory
                                                                                                                                                              1. Environmental Epigenetics

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                                                                                                                                                          1. Foundations of Plant Molecular Biology

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                                                                                                                                                          3. Gene Expression and Its Regulation