Genomics News Oak Research

PhD studentship: Genomics of oak trees and their microbiota

I have just advertised a new PhD studentship opportunity on I am really excited about this project, and we have a huge amount on data already in hand for the new student to analyse. Here is the project description:

Oaks are the most common trees in England, and of huge ecological, economic and cultural value. They support large communities of microbes, some of which are beneficial and some of which are pathogenic. Oaks are affected by health problems including acute oak decline, chronic oak decline, mildews, and honey fungus. This project will use whole genome sequence data for oak trees and their microbiomes to investigate factors affecting oak health. In collaboration with Royal Botanic Gardens Kew and Forest Research we have just generated short read sequence data for the genomes and leaf microbiomes of 400 oak trees from five UK populations. We are seeking a talented student to analyse these data. The project will uncover the population diversity of English oak trees and their microbiota and begin to understand the genetic component of oak health problems. Around 60% of the project will involve bioinformatic analyses including read-mapping to reference genomes, SNP calling, diversity analyses, and database searching. The student will graduate with a highly transferable set of genomic bioinformatics skills that will be applicable to all genomics projects including human medical genomics. Around 10% of the project will consist of fieldwork, phenotyping oak trees in UK populations. About 30% of the project will consist of writing papers and attending genomics conferences. The student will join a team of researchers working on the genomics of broad-leaved trees who will provide training on the techniques needed for the project. This is an exciting project with significant stakeholder interest. In the past, it has been hard to do genetic research on oak trees due to their long generation times and large size. We hope that by using novel genomic approaches first developed for humans we can make rapid progress in understanding the genetic component of oak susceptibility to pathogens.

This studentship is funded by UK Department for Environment, Food and Rural Affairs and Royal Botanic Gardens, Kew. The studentship is open to UK and EU applicants. It will cover tuition fees and provide an annual tax-free maintenance allowance for 3 years at Research Councils UK rate (£16,553 in 2017/18).

You can apply online on the Queen Mary University of London website here.