University of Leeds Featured PhD Programmes
Norwich Research Park Featured PhD Programmes
Norwich Research Park Featured PhD Programmes
University of Dundee Featured PhD Programmes
University of Bristol Featured PhD Programmes

Genomic analysis of the parasitic nematode Phasmarhabditis hermaphrodita (and other wild Phasmarhabditis species) – a biological control agent of slugs

  • Full or part time
  • Application Deadline
    Friday, November 22, 2019
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Project Description

Understanding the genetic determinants of key traits in parasitic organisms provides important tools for developing novel pest control products. Slugs are serious pests in agriculture and a persistent problem for home gardens. They are commonly controlled using pesticide pellets, but as these can have negative effects on non-target organisms, including pets and wildlife, a more sustainable and ecologically sound alternative was developed. This is the nematode Phasmarhabditis hermaphrodita, a facultative parasite of slugs and snails. P. hermaphrodita was formulated into a biological control agent (Nemaslug®) by BASF Agricultural Specialties for use by farmers and gardeners and since 1994 has been used regularly in the U.K. and Europe, provide significant protection against slugs. However, there are reports that P. hermaphrodita cannot kill larger pestiferous slug species. In order to better understand key traits such as virulence, longevity, stress tolerance and dispersal to improve the Nemaslug® product, the student will apply cutting-edge genomic technologies to sequence the genomes of P. hermaphrodita (Nemaslug®) and other Phasmarhabditis species isolated from the wild. The student will undertake genomic analyses of these nematodes, including genome assembly and annotation and comparative genomic analysis with other nematodes.

i) Whole genome sequencing and annotation of Phasmarhabditis hermaphrodita

The genome of the strain of P. hermaphrodita currently used in the production of Nemaslug® (called DMG0001) will be sequenced using a combination of long read (Pacific BioSciences) and short read (Illumina) sequencing technologies. Whole transcriptome RNA sequencing will also be done to aid gene annotation. The student will assemble and annotate the genome. In addition to this reference genome for P. hermaphrodita, 10 strains recently isolated from the wild and kept in culture at LJMU will be re-sequenced and mapped to the reference genome for population and evolutionary genomic analysis. Candidate genes involved in virulence, longevity and stress tolerance will be tested in lab experiments carried out in parallel.

ii) Whole genome sequencing of other Phasmarhabditis species (P. californica and P. neopapillosa) isolated from the wild

In addition to P. hermaphrodita, the student will sequence the genomes of other Phasmarhabditis species, allowing comparative analyses of the genetics of virulence and other traits. 5 P. neopapillosa and 3 P. californica wild isolates currently in culture in LJMU will be sequenced (genomes and transcriptomes), assembled and annotated as for P. hermaphrodita. A genome exploration system will be developed to allow browsing and further investigation.

Ultimately, this project will provide the tools to enable genomic/genetic improvement of P. hermaphrodita as a biological control agent, as well as investigating the potential of other Phasmarhabditis species to be developed as alternative products.
The project will provide an excellent opportunity for the student to apply state-of-the-art genome bioinformatics tools and technologies to advance knowledge of and improve an important biological pest control tool.

Qualifications/ Skills Required:

The candidate requires a 2:1 degree or above in a relevant subject area. A relevant MSc qualification is desirable, but not essential.

The candidate must have experience in bioinformatics. The project will suit a candidate with a firm knowledge of genomics and computational biology. Practical wet-lab experience and the ability to work independently are desirable, as is a knowledge and understanding of parasitology, particularly nematology.

Full training will be provided to the candidate along with access to the broad knowledge and expertise held by the supervisory team.

Funding Notes

This studentship is funded by BASF. Only UK & EU citizens can apply for this studentship. Funding will consist of full tuition fees for three years and the award of a living stipend at UK Research Council rates.

References

Informal enquiries are welcome. Applicants should email a CV, covering letter detailing their suitability for the project and contact details of two referees to Dr Robbie Rae: [email protected] and Dr. Gareth Weedall: [email protected]

Email Now

Insert previous message below for editing? 
You haven’t included a message. Providing a specific message means universities will take your enquiry more seriously and helps them provide the information you need.
Why not add a message here
* required field
Send a copy to me for my own records.

Your enquiry has been emailed successfully





FindAPhD. Copyright 2005-2019
All rights reserved.