Plant-parasitic nematodes: from genomics to functional analysis of parasitism genes

Nematodes (roundworms) belong to the largest phylum on earth. The numerous species inhabit practically all ecological niches, including plants. Plant-parasitic species live on plant roots, causing substantial damage to the plant and hampering its development. As such, they cause gigantic economical losses in crop production. We used a molecular approach to analyze the plant-parasitic nematode Radopholus similis by generating expressed sequence tags (ESTs). The most striking discovery was tags corresponding to aWolbachia-like endosymbiont, which was subsequently located in the ovaria of R. similis. Numerous tags corresponding to parasitism genes with potential roles in, amongst other things, host localisation, detoxification, cell wall modification, and even putative host transcriptional reprogramming were identified. In addition, a tool to explore all available nematode EST data is presented in this study. The ‘nematode EST exploration tool’ (NEXT) (http://zion.ugent.be/joachim/next) extends the usefulness by extracting and storing temporal and spatial information of all publicly available nematode EST libraries. Some members of the transthyretin-like gene family of R. similis were characterized. All stages except developing embryos express the analyzed genes, and expression is localized to the ventral nerve cord and tissues surrounding the vulva. Predicted secondary structure is suggestive of a binding capacity with a yet unknown ligand. Further, the annotation of the complete mitochondrial (mt) genome of R. similis is reported. The mt genome has the expected gene content, but shows many aberrant features such as: a considerably smaller 16S rRNA with reduced structures, two large repeat regions, the lack of stop codons on many genes and a unique codon reassignment UAA:Stop to UAA:Tyrosine. The aberrant features in the mt genome could be related to this codon reassignment, but results are ambiguous and require further research. A last part of the study reports on the response of the plant on nematode infection. Signaling of two plant hormones involved in plant defense is measured during early phases of parasitism. In addition, the role of flavonoid compounds produced by the plant is analyzed by infection tests on several mutants