Name: Paul Wilkinson
Institution: University of Exeter
Research: mRNA analysis
Pesticide resistance is becoming more of a problem throughout the world as the use of pesticides continues. Pesticides that were once effective at killing crop pests are now no longer effective leading to an increase in damaged or destroyed crops. One group of researchers at the University of Exeter are using the NGS to try and understand how this resistance is developed.
Paul and his research group are analyzing the transcriptomes of insects that are major crop pests, such as Manduca sexta, the tobacco hornworm moth. A transcriptome is the set of all messenger RNA (mRNA) molecules, or "transcripts," that are produced in a population of cells and reflects the genes that are actively expressed at any given time.
The entire transcriptome of an insect pest is sequenced using the latest ‘Next generation’ DNA sequencing technologies. Assembling this sequence data generates in excess of 40,000 sequences which are then annotated by comparing the expressed sequences against known protein sequences contained in protein databases such as UniProt.
Paul explained that “sequencing transcriptomes can help scientists to understand how insects develop resistance to pesticides. By looking at changes in genes that code for proteins involved in the metabolic pathways that detoxify pesticides; we can assess how resistant insect strains evolve in the field. In addition the availability of a fully annotated transcriptome allows us to examine differential gene expression of these pesticide resistance genes, using the recently developed digital transcriptomics technologies”. It is also hoped that the sequencing of insect transcriptomes will lead to the discovery of new enzymes that could be used industrially for such things as biofuels, fruit juice extraction / clarification and waste water treatment.
The homology searches are performed at NGS using the NCBI BLAST software. This is a parallel implementation of NCBI BLAST that distributes computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O.
Paul’s team are also planning on using mpiBLAST which they hope will improve NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. This should dramatically reduce the length of time required to characterise all of the expressed genes in our insect transcriptomes.
Paul said "The NGS staff have been a great help to us in the implementation of our high-throughput BLAST’s. Homology searches had always been the bottleneck in our data analysis pipeline. Making use of the NGS resources has significantly reduced the time it takes to process our data".
Image courtesy of Jan Stipala at the University of Exeter.
For more technical details on Pauls use of NGS resources please see the December 2009 edition of NGS NEWS
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