Genomics and Molecular Genetics of Plant-Nematode Interactions

Part I - Introductory Chapters. 1. Introduction to Plant-parasitic Nematodes; Modes of Parasitism. 1.1. Introduction to Nematodes. 1.2. Evolution of Plant Parasitism. 1.3. Hatching. 1.4. Attraction to Plants. 1.5. Penetration and Feeding. 1.6. Moulting. 1.7. Reproduction. 1.8. Survival. 1.9. Conclusions. 2. Current nematode threats to world agriculture. 2.1 Key nematodes threatening major agricultural crops of importance worldwide. 2.2 Quarantine nematodes of global importance. 2.3 Key nematodes on food staples for food security in developing countries. 3. Phylogeny and evolution of nematodes. 3.1 Introduction. 3.2 Backbone of nematode phylogeny. 3.3 Phylogeny of Tylenchomorpha. 3.4 Tylenchomorpha - top end plant parasites. 3.5 Concluding remarks. 4. Cyst nematodes and syncytia. 4.1 Introduction. 4.2 Root invasion and selection of the initial syncytial cell. 4.3 Syncytium development. 4.4 Syncytium ultrastructure. 4.5 Defence responses. 4.6 Concluding remarks. 5. Root-knot nematodes and giant cells. 5.1 Introduction. 5.2 Root invasion and migration. 5.3 Giant cell formation and function. 5.4 Giant cell induction - a deliberate controlled event. 5.5 Host resistance to root-knot nematodes. 5.6 Concluding remarks. Part II - Resources for functional analysis of plant-nematode interactions. 6. Genome analysis of plant parasitic nematodes. 6.1 Introduction. 6.2 Sequencing strategies. 6.3 Genome organization. 6.4 Plant parasitism. 6.5 Gene family and pathway conservation and diversification among plant parasitic and free-living nematodes. 6.6 Tools for functional genomics and genetics. 6.7 Future prospects sequencing of parasitic nematode genomes. 7. Transcriptomes of plant-parasitic nematodes. 7.1 Introduction. 7.2 Intra-specific transcriptomics has proven a powerful approach to identify parasitism-related genes. 7.3 Expressed sequence tags, the most versatile source of molecular data for plant parasitic nematodes. 7.4 Web-Based Access to Plant Parasitic Nematode EST data and tools to support analysis. 7.5 Functional and structural characterization of ESTs: understanding the molecular basis of parasitism. 7.6 Pan-phylum transcriptomics: an approach that reveals broadly conserved and taxonomically restricted molecular features in Nematoda. 7.7 The future of plant parasitic nematode transcriptomics. 8. Arabidopsis as a tool for the study of plant-nematode interactions. 8.1. Why Arabidopsis was the best choice for molecular approaches to plant-nematode interactions: a historical perspective. 8.2. Findings that were possible because of Arabidopsis. 8.3. High expectations that never quite made true. 8.4. When it would be better to use other model systems. 8.5. Future prospects: will Arabidopsis still be the best or only choice?. 9. Transcriptomic and proteomic analysis of the plant response to nematode infection. 9.1. Parasitic nematode interaction with plants. 9.2. A historical view of methods used to study transcriptional changes during plant-nematode interactions. 9.3. Microarray analysis of nematode-infected root tissues. 9.4. Next generation sequencing technology to study plant responses to nematode infection. 9.5. Proteomic analysis of the plant response to nematode infection. 9.6. Conclusions. 10. C. elegans as a resource for studies on plant parasitic nematodes. 10.2. C. elegans as a model nematode. 10.3. Application of RNAi in C. elegans and parasitic nematodes. 10.4. General conclusion and future perspectives. 11. Parallels between plant and animal parasitic nematodes. 11.1 Introduction. 11.2 Morphology. 11.3 Life Histories. 11.4. Neuronal Signalling Systems. 11.5. Endosymbionts. 11.6. Host-Parasite Interactions. 11.7. Concluding Remarks. Part III - Molecular genetics and cell biology of plant-nematode interactions. 12. Degradation of the plant cell wall by nematodes. 12.1 Introduction. 12.2 Enzymatic degradation of plant cell walls. 12.3 Non-enzymatic modification of plant cell walls. 12.4 Degradation of fun