Location: Floral and Nursery Plants ResearchTitle: Characterization of the Pratylenchus penetrans transcriptome including data mining of putative nematode genes involved in plant parasitism
|VIEIRA, PAULO - Virginia Tech|
|EVES-VAN DEN AKKER, SEBASTIAN - University Of Dundee|
|VERMA, RUCHI - Orise Fellow|
|WANTOCH, SARAH - Virginia Tech|
|EISENBACK, JONATHAN - Virginia Tech|
Submitted to: PLoS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2015
Publication Date: 12/14/2015
Publication URL: http://handle.nal.usda.gov/10113/61755
Citation: Vieira, P., Eves-Van Den Akker, S., Verma, R., Wantoch, S., Eisenback, J.D., Kamo, K.K. 2015. Characterization of the Pratylenchus penetrans transcriptome including data mining of putative nematode genes involved in plant parasitism. PLoS One. 10(12):e0144674. doi: 10.1371/journal.pone.0144674.
Interpretive Summary: Worldwide crop losses due to plant-parasitic nematodes have been estimated at $118 billion annually, with root lesion nematodes, Pratylenchus spp., ranking third in terms of economic losses. The root lesion nematode P. penetrans is considered one of the most economically important species within the genus, and host range studies had shown that nearly 400 plant species can be parasitized by P. penetrans. We report an overall analyses of the transcriptome of P. penetrans, and explore the efficacy of RNAi, delivered from the host, as a strategy to control the migratory nematode P. penetrans by targeted knockdown of selected nematode genes. The transcriptome analysis enabled the identification of putative “parasitism genes” based on differential expression and specific up-regulation during the early phases of plant infection. This information will contribute to a better understanding of the interactions between P. penetrans and its host plant that could lead to effective control strategies for this nematode species.
Technical Abstract: The root lesion nematode Pratylenchus penetrans is considered one of the most economically important species within the genus. Host range studies have shown that nearly 400 plant species can be parasitized by this species. To obtain insight into the transcriptome of this migratory plant-parasitic nematode, we used Illumina mRNA sequencing analysis of a mixed population, as well as nematode reads detected in infected soybean roots 3 and 7 days after nematode infection. Over 140 million paired end reads were obtained for this species, and de novo assembly resulted in a total of 23,175 transcripts. Homology searches showed significant hit matches to 58% of the total number of transcripts using different protein and EST databases. In general, the transcriptome of P. penetrans follows common features reported for other root lesion nematode species. We also explored the efficacy of RNAi, delivered from the host, as a strategy to control P. penetrans, by targeted knock-down of selected nematode genes. Comparisons were made to identify putative nematode genes with a role in parasitism, resulting in the identification of transcripts with similarities to other nematode parasitism genes. Focusing on the predicted nematode secreted proteins found in this transcriptome, we observed specific genes to be up-regulated at the early time points of infection. In the present study, we observed an enrichment of predicted secreted proteins along the early time points of parasitism by this species, with a significant number being pioneer candidate genes. A representative set of genes examined using RT-PCR confirms their expression during the host infection. The expression patterns of the different candidate genes raises the possibility that they might be involved in critical steps of P. penetrans parasitism. This analysis sheds light on the transcriptional changes that accompany plant infection by P. penetrans, and will aid in identifying potential gene targets for selection and use to design effective control strategies against root lesion nematodes.