Pathogen infection of crops causes large-scale annual yield losses for farmers worldwide and hinders global efforts to provide adequate amounts of nutrition for the ever-growing human population. Plant-parasitic nematodes (PPN) are among some of the most devastating pathogens due to their ability to parasitize an expansive variety of agriculturally important crops. In order to identify ways to attenuate PPN infection and limit yield losses it is vital that we increase our understanding of host-PPN interactions. Here we investigate the molecular mechanisms that are occurring both within PPN and at the interface between PPN and their host plants.

Research into PPN-derived secretory proteins, termed effectors is currently the most well studied avenue of research to date. Discoveries made as part of this dissertation make a significant contribution to PPN effector research by identifying the first DNA-binding PPN effector and characterizing its functionality in the model PPN-host system Heterodera schachtii, the sugar beet cyst nematode, and Arabidopsis thaliana.

The secretion of exosomes and small RNAs from a number of pathogens into their respective hosts, including animal parasitic nematodes, led us to investigate these potential mechanisms in PPN. Exploration into exosome secretion in two different PPN species yielded a small and inconsistent number of exosome-like vesicles. It became apparent that isolation of exosomes from obligate parasites such as PPN poses a number of technical challenges making it impossible to conclude that the release of exosomes is a bone-fide parasitic strategy utilized by PPN. High-throughput small RNA sequencing of H. glycines led to the detection of a set of PPN-derived miRNAs that have the potential to target host plant transcripts. Future verification of the functionality of PPN-derived miRNAs within host cells will represent a major breakthrough in our understanding of PPN infection.

Finally, we investigated the role of spliced leader trans-splicing (SLTS) in Heterodera glycines, the soybean cyst nematode. The existence of spliced leaders (SL) within the nematode phylum was documented several decades ago but it is still unclear what role SLTS plays within the nematode and how vital this role is to nematode viability. A comprehensive genome and transcriptome-wide SL study was conducted in H. glycines, which identified a large set of hypervariable SLs that were collectively found on >2,000 transcripts. The frequent appearance of H. glycines SLs on a large number of transcripts makes them an attractive target for future RNAi studies aimed at significantly affecting the viability of H. glycines.

Collectively, the research presented in this dissertation furthers our understanding of currently explored parasitic mechanisms and offers plausible insights into promising new avenues of PPN research.