The Pratylenchus penetrans transcriptome as a source for the development of alternative control strategies

mining for putative genes involved in parasitism and evaluation of in planta RNAi

Paulo Vieira (Lead / Corresponding author), Sebastian Eves-Van Den Akker, Ruchi Verma, Sarah Wantoch, Jonathan D. Eisenback, Kathryn Kamo

Research output: Contribution to journalArticle

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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 23,715 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. Different comparisons were performed 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 members 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 RTPCR confirms their expression during the host infection. The expression patterns of the different candidate genes raise 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.

Original languageEnglish
Article number0144674
Number of pages25
JournalPLoS ONE
Volume10
Issue number12
DOIs
Publication statusPublished - 14 Dec 2015

Fingerprint

Pratylenchus penetrans
RNA Interference
Plantae
Transcriptome
transcriptome
parasitism
Genes
root lesion nematodes
Nematoda
genes
Infection
infection
Nematode Infections
Protein Databases
Proteins
proteins
nematode infections
Host Specificity
Expressed Sequence Tags
plant parasitic nematodes

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Vieira, Paulo ; Eves-Van Den Akker, Sebastian ; Verma, Ruchi ; Wantoch, Sarah ; Eisenback, Jonathan D. ; Kamo, Kathryn. / The Pratylenchus penetrans transcriptome as a source for the development of alternative control strategies : mining for putative genes involved in parasitism and evaluation of in planta RNAi. In: PLoS ONE. 2015 ; Vol. 10, No. 12.
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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 23,715 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. Different comparisons were performed 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 members 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 RTPCR confirms their expression during the host infection. The expression patterns of the different candidate genes raise 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.",
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The Pratylenchus penetrans transcriptome as a source for the development of alternative control strategies : mining for putative genes involved in parasitism and evaluation of in planta RNAi. / Vieira, Paulo (Lead / Corresponding author); Eves-Van Den Akker, Sebastian; Verma, Ruchi; Wantoch, Sarah; Eisenback, Jonathan D.; Kamo, Kathryn.

In: PLoS ONE, Vol. 10, No. 12, 0144674, 14.12.2015.

Research output: Contribution to journalArticle

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