Rhizobium Genetics and Plasmid Biology

  1. Plasmid Evolution and Horizontal Gene Transfer
    1. Mechanisms of Horizontal Transfer
      1. Conjugative Transfer
        1. Self-transmissible plasmids
          1. Mobilizable plasmids
            1. Transfer frequencies
            2. Transformation
              1. Natural competence
                1. Artificial transformation
                  1. DNA uptake mechanisms
                  2. Transduction
                    1. Generalized transduction
                      1. Specialized transduction
                        1. Phage-mediated transfer
                      2. Mobile Genetic Elements
                        1. Insertion Sequences
                          1. IS element families
                            1. Transposition mechanisms
                              1. Target site selection
                              2. Transposons
                                1. Composite transposons
                                  1. Tn5 and Tn10 families
                                    1. Antibiotic resistance genes
                                    2. Integrative Conjugative Elements
                                      1. ICE characteristics
                                        1. Integration mechanisms
                                          1. Excision and transfer
                                          2. Genomic Islands
                                            1. Symbiosis islands
                                              1. Pathogenicity islands
                                                1. Metabolic islands
                                              2. Plasmid Evolution Patterns
                                                1. Modular Evolution
                                                  1. Functional modules
                                                    1. Recombination hotspots
                                                      1. Module shuffling
                                                      2. Host Range Evolution
                                                        1. Adaptation mechanisms
                                                          1. Specificity changes
                                                            1. Coevolution patterns
                                                            2. Plasmid-Chromosome Interactions
                                                              1. Integration events
                                                                1. Chromosomal rearrangements
                                                                  1. Gene transfer
                                                                2. Symbiotic Gene Transfer
                                                                  1. Sym Plasmid Mobility
                                                                    1. Transfer to new hosts
                                                                      1. Host range expansion
                                                                        1. Symbiotic competence
                                                                        2. Chromosomal Integration
                                                                          1. Integration mechanisms
                                                                            1. Stability consequences
                                                                              1. Evolutionary implications
                                                                              2. Novel Symbioses
                                                                                1. Host jumping events
                                                                                  1. Adaptation processes
                                                                                    1. Ecological impacts

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                                                                                6. Plasmid Molecular Biology

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                                                                                8. Genetic Analysis and Molecular Tools