Analysis of the genomics of Pratylenchus vulnus, a plant parasitic nematode, and its interaction with walnut roots

Pratylenchus vulnus, a root lesion nematode, is a migratory endoparasite that feeds on the roots of many plants, including fruit and nut trees. In California, it is an important parasite of walnut (Juglans spp.). This research characterized gene expression patterns in P. vulnus and in walnut associated with the early stages of nematode parasitism to investigate the response of a susceptible host plant.;Through the sequencing of mixed-stage P. vulnus transcripts, 5,218 expressed tag sequences (ESTs) were generated and compiled into a set of 2,733 unique genes. Over 60% of the P. vulnus genes were annotated as orthologs of sequences identified in other organisms, including the free-living nematode Caenorhabditis elegans. Seventeen genes were identified as candidates for acquisition by horizontal gene transfer from bacteria, which might have been an important mechanism in the evolution of plant-parasitic nematodes. A group of 181 genes exclusively common to P. vulnus and other plant parasites are candidates for further study as targets for novel nematicides.;Eight P. vulnus genes, whose orthologs in C. elegans have consistent and desirable RNAi phenotypes, were targeted for suppression with dsRNA in multiple soaking experiments. Transcript levels of seven genes were significantly reduced as determined by real time quantitative RT-PCR. However, seasonal variation in the experimental results was significant.;A Paradox (Px1) rootstock clone derived from an interspecific cross of California black and Persian walnut (J. hindsii x J. regia) and susceptible to P. vulnus infection was examined for changes in gene expression induced by nematode feeding. Six cDNA libraries were constructed from the leaves and roots of infected and uninfected plants to generate 13,559 ESTs. These ESTs, combined with 5,040 existing walnut sequences, were compiled into an annotated set of 8,622 unique genes, which were used to design microarrays. Analysis of gene expression in leaves and roots of nematode-infected and control Px1 plants showed a distinct pattern of gene expression in which some defense related genes are up-regulated, particularly in the earliest stages of infection, while many more such genes are suppressed. Genes whose expression is consistently altered by P. vulnus parasitism may be candidate molecular markers of nematode susceptibility and may be useful in molecular tests to diagnose infected but asymptomatic trees.;Roots of Medicago truncatula A17, a legume host for P. vulnus, were inoculated with nematodes and were harvested 17 days later. Comparison of gene expression between roots of infected and control plants using Affymetrix Medicago GeneChipsRTM identified very few differentially expressed genes, comparable to that seen at the earliest time point of the Px1 experiment. Several of these genes were orthologs of walnut genes with similar expression patterns.