current PROjects
- Development of quantitative molecular assays for the identification and quantification of Meloidogyne spp.
- Population genetics of economically important plant-parasitic nematodes including Radopholus similis and Heterodera humulii
- New nematode genomes including: Globodera ellingtonae, Anguina agrostis, Pratylenchus neglectus, P. penetrans, P. thornei, and Xiphinema americanum
- Phylogenetics of the Xiphinema americanum species complex
- Development of robust and inclusive primers for the detection of nepoviruses in plants and nematodes
past projects
Genomes sequencing project. - This ongoing multifaceted project is a collaborative effort with the Denver Lab at Oregon State University. Briefly, the aim of this project is to provide the plant-parasitic nematology community with genomic data for agriculturally important species.
We have used high throughput sequencing methods to sequence the genomes from six plant parasitic nematode species (Anguina agrostis, Globodera ellingtonae, Pratylenchus neglectus, P. penetrans, P. thornei, and Xiphinema americanum) and are currently working on assembly of the genomes. Additionally, research is underway to investigate potential homologues and/or paralogues of ten different effector genes within the sequence data generated thus far. Finally, genome skimming revealed symbiotic bacterium within some of the nematodes we sequenced. Results from these latest analyses can found be here.
Globodera ellingtonae - We are using PacBio and Miseq sequencing data to assemble the G. ellingtonae genome in collaboration with the Denver lab. As part of that, analysis of the multi-circle mitochondrial genome is underway. A transcriptome from combined life stages has been assembled. Future work includes annotation of the genome, analysis of differential gene expression during infection, and localization of effector genes during infection.
Molecular identification of Pratylenchus species. - We have developed molecular tools to identify P. crenatus, P. neglectus, P. penetrans, and P. thornei individuals to species via PCR. Species specific primer sets were developed, tested, and optimized for each of the aforementioned species. These new primers are unique in that they each amplify a uniquely sized amplicon from each target.
Phylogenetic studies of individuals within the Xiphinema americanum species complex. - We used high throughput sequencing to examine two regions of ribosomal DNA as well as the mitochondrial genome of Xiphinema americanum from twelve geographically disparate populations across the U.S.. Sequence data was obtained from multiple individuals from each population. Results from this work can be found here.