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 - 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 fungal cell walls. 12.5 Evolutionary aspects of cell wall modifying proteins. 12.6 Concluding remarks. 13. Suppression of plant defences by nematodes. 13.1 Plant parasitic nematodes as biotrophic pathogens. 13.2 Protection of the feeding site (biotrophy). 13.3 Protection of the nematode. 13.4 Conclusions and future prospects. 14. Other nematode effectors and evolutionary constraints. 14.1 A wide range of effectors are secreted during parasitism. 14.2 Signalling and protection at the plant-nematode interface. 14.3 Stylet secretions are major parasitism effectors. 14.4 Nematode effectors can trigger plant resistance. 14.5 Evolution of nematode effectors. 15. Disease resistance-genes and defense responses during incompatible interactions. 15.1 Introduction. 15.2 Nematode resistance genes. 15.3 Defense responses during incompatible interactions. 15.4 Resistance mechanisms. 15.5 Concluding remarks. 16. The role of plant hormones in nematode feeding cell formation. 16.1 Introduction. 16.2 Phytohormone-associated gene expression profiles in feeding cell formation. 16.3 Auxin. 16.4 Ethylene. 16.5 Cytokinin. 16.6. Peptide hormones. 16.7. Perspectives. 17. Unravelling the plant cell cycle in nematode induced feeding sites. 17.1 Introduction. 17.2. Transcriptional activity and transcript levels of cell cycle genes in nematode feeding sites. 17.3 In situ profiling of cell cycle genes in uninfected Arabidopsis: a useful source of information for nematode feeding sites. 17.4 DNA synthesis and the endocycle in the multinucleate giant cells and syncytia. 17.5 Cell Cycle inhibitors influence DNA synthesis and mitosis in feeding cells. 17.6 Concluding remarks. 18. The plant cytoskeleton remodelling in nematode induced feeding sites. 18.1. Introduction. 18.2. Actin and tubulin genes are highly expressed in nematode feeding sites. 18.3. Cytoskeleton rearrangements in nematode feeding sites. 18.4 The effects of cytoskeleton-disrupting drugs on nematode feeding sites. 18.5. Cytoskeleton interacting proteins and their putative role in feeding site development. 18.6. Closing remarks. 19. 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 fungal cell walls. 12.5 Evolutionary aspects of cell wall modifying proteins. 12.6 Concluding remarks. 13. Suppression of plant defences by nematodes. 13.1 Plant parasitic nematodes as biotrophic pathogens. 13.2 Protection of the feeding site (biotrophy). 13.3 Protection of the nematode. 13.4 Conclusions and future prospects. 14. Other nematode effectors and evolutionary constraints. 14.1 A wide range of effectors are secreted during parasitism. 14.2 Signalling and protection at the plant-nematode interface. 14.3 Stylet secretions are major parasitism effectors. 14.4 Nematode effectors can trigger plant resistance. 14.5 Evolution of nematode effectors. 15. Disease resistance-genes and defense responses during incompatible interactions. 15.1 Introduction. 15.2 Nematode resistance genes. 15.3 Defense responses during incompatible interactions. 15.4 Resistance mechanisms. 15.5 Concluding remarks. 16. The role of plant hormones in nematode feeding cell formation. 16.1 Introduction. 16.2 Phytohormone-associated gene expression profiles in feeding cell formation. 16.3 Auxin. 16.4 Ethylene. 16.5 Cytokinin. 16.6. Peptide hormones. 16.7. Perspectives. 17. Unravelling the plant cell cycle in nematode induced feeding sites. 17.1 Introduction. 17.2. Transcriptional activity and transcript levels of cell cycle genes in nematode feeding sites. 17.3 In situ profiling of cell cycle genes in uninfected Arabidopsis: a useful source of information for nematode feeding sites. 17.4 DNA synthesis and the endocycle in the multinucleate giant cells and syncytia. 17.5 Cell Cycle inhibitors influence DNA synthesis and mitosis in feeding cells. 17.6 Concluding remarks. 18. The plant cytoskeleton remodelling in nematode induced feeding sites. 18.1. Introduction. 18.2. Actin and tubulin genes are highly expressed in nematode feeding sites. 18.3. Cytoskeleton rearrangements in nematode feeding sites. 18.4 The effects of cytoskeleton-disrupting drugs on nematode feeding sites. 18.5. Cytoskeleton interacting proteins and their putative role in feeding site development. 18.6. Closing remarks. 19. Cell wall modifications induced by nematodes. 19.1 Introduction. 19.2 Ultrastructure of feeding site wall in susceptible interactions. 19.3 Expression of genes involved in cell wall extension and remodeling. 19.4 Expression of genes involved in cell wall degradation in NFS. 19.5 Expression of genes involved in cell wall biosynthesis in NFS. 19.6 Ultrastructure of feeding site wall in resistant interactions. 19.7 Nematode development and cell wall modifications in plants with silenced expression of cell wall-related genes. 19.8 Summary. 20. Water and nutrient transport in nematode feeding sites.- 20.1 Nematodes as obligate parasites depend on plant water and solute supply.- 20.2 Water transport.- 20.3 Solute supply of nematode-induced feeding structures.- 20.4 Other plant-nematode interactions.- 20.5 Nematode feeding.- 20.6 Nutrient cycling and limited nutrient supply.- 20.7 Conclusions.- Part IV - Applied aspects of molecular plant nematology: exploiting genomics for practical outputs. 21. Molecular tools for diagnostics. 21.1 Introduction. 21.2 Markers for PCR diagnostics. 21.3 Other diagnostic methods. 21.4 Soil PCR. 21.5. Validation and troubleshooting. 21.6. Future research and perspectives. 21.7. Conclusions. 22. Breeding for nematode resistance: use of genomic information. 22.1 Introduction. 22.2: Mapped nematode resistance genes and QTLs. 22.3: Molecular marker-assisted breeding for resistance to nematodes. 22.4: Genes underlying resistance to nematodes. 22.5: Breeding for durable resistance to nematodes. 22.6 Conclusions. 23. Biological Control of Plant-Parasitic Nematodes: Towards Understanding Field Variation Through Molecular Mechanisms. 23.1 Introduction. 23.2 Ecological Context. 23.3 Molecular approaches for assessing field biodiversity. 23.4 Towards understanding field variation through molecular mechanisms: three models. 23.5 Future developments. 24. Nematode resistant GM crops in industrialised and developing countries. 24.1 Introduction. 24.2 Manipulation of Plant Resistance. 24.3 Development of biotechnological solutions to nematode control. 24.4 Progress towards transgenic resistance in crop plants. 24.5 Future developments. 24.6 Prospects for implementation of biotechnological control.