Plant Genetics and Molecular Biology

  1. Plant Genomics and Bioinformatics
    1. Genome Sequencing Technologies
      1. Sanger Sequencing
        1. Chain Termination Method
          1. Applications and Limitations
          2. Next-Generation Sequencing
            1. Short-Read Platforms
              1. Illumina Sequencing
                1. Ion Torrent
                2. Applications in Plant Genomics
                  1. Whole Genome Sequencing
                    1. Transcriptome Sequencing
                  2. Long-Read Sequencing
                    1. Third-Generation Sequencing Technologies
                      1. PacBio SMRT
                        1. Oxford Nanopore
                        2. Advantages and Limitations
                          1. Hybrid Assembly Approaches
                        3. Genome Assembly and Annotation
                          1. Assembly Algorithms
                            1. Overlap-Layout-Consensus
                              1. De Bruijn Graph Approaches
                                1. Hybrid Assembly Methods
                                2. Quality Assessment
                                  1. Assembly Metrics
                                    1. Completeness Evaluation
                                    2. Gene Prediction Methods
                                      1. Ab Initio Gene Prediction
                                        1. Evidence-Based Prediction
                                          1. Comparative Gene Prediction
                                          2. Functional Annotation
                                            1. Homology-Based Annotation
                                              1. Domain-Based Annotation
                                                1. Pathway Analysis
                                              2. Functional Genomics
                                                1. Transcriptomics
                                                  1. RNA-Seq Workflow
                                                    1. Library Preparation
                                                      1. Sequencing and Quality Control
                                                      2. Differential Gene Expression Analysis
                                                        1. Statistical Methods
                                                          1. Multiple Testing Correction
                                                          2. Alternative Splicing Analysis
                                                          3. Proteomics
                                                            1. Protein Identification and Quantification
                                                              1. Mass Spectrometry Methods
                                                                1. Protein Database Searching
                                                                2. Post-Translational Modification Analysis
                                                                  1. Phosphoproteomics
                                                                    1. Glycoproteomics
                                                                  2. Metabolomics
                                                                    1. Metabolite Profiling
                                                                      1. Targeted Metabolomics
                                                                        1. Untargeted Metabolomics
                                                                        2. Data Analysis Approaches
                                                                          1. Statistical Analysis
                                                                            1. Pathway Mapping
                                                                        3. Comparative Genomics
                                                                          1. Synteny and Collinearity
                                                                            1. Identification and Analysis
                                                                              1. Synteny Visualization Tools
                                                                              2. Evolutionary Analysis
                                                                                1. Phylogenetic Methods
                                                                                  1. Tree Construction
                                                                                    1. Molecular Evolution
                                                                                    2. Genome Duplication Events
                                                                                      1. Whole Genome Duplications
                                                                                        1. Segmental Duplications
                                                                                    3. Bioinformatics Tools and Databases
                                                                                      1. Sequence Alignment Tools
                                                                                        1. BLAST
                                                                                          1. BLAST Algorithms
                                                                                            1. Database Searching
                                                                                            2. Multiple Sequence Alignment
                                                                                              1. Progressive Alignment
                                                                                                1. Iterative Methods
                                                                                              2. Gene Ontology
                                                                                                1. Structure and Use
                                                                                                  1. Biological Process
                                                                                                    1. Molecular Function
                                                                                                      1. Cellular Component
                                                                                                      2. Functional Annotation
                                                                                                        1. Enrichment Analysis
                                                                                                        2. Plant Genome Databases
                                                                                                          1. Model Plant Databases
                                                                                                            1. TAIR for Arabidopsis
                                                                                                              1. Rice Genome Annotation Project
                                                                                                              2. Crop Genome Databases
                                                                                                                1. Phytozome
                                                                                                                  1. Gramene

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                                                                                                            8. Genetic Engineering and Plant Biotechnology