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Precision Medicine DTP - Genomic analysis of the impact of sexual recombination on the segregation of virulence genes in African trypanosomes

Project Description


African trypanosomes are vector-borne protozoa that cause serious human and animal disease across sub-Saharan Africa. Trypanosomes cause chronic, debilitating and fatal infections, and are able to do this in large part due to their extremely elaborate antigenic variation system. This is mediated by one species of protein, the variant surface glycoprotein (VSG), of which there are over 2,000 gene copies in the genome of Trypanosoma brucei. Antigenic variation is achieved by sequentially changing the identity of the expressed VSG, thereby staying one step ahead of the host immune response1. T. brucei can undergo sexual recombination in the insect vector2, and therefore mixing of the genome and VSG repertoire via meiotic recombination in the progeny. Until recently, the ability to resolve and confidently assemble the genomic VSG repertoire, which exists mostly in extensive hemizygous sub-telomeric gene arrays, has been very limited. However, tools have become available that now make this possible3. The supervisors have generated cloned F1 progeny resulting from sexual recombination between two T. brucei strains. In this project, the student will analyse the inheritance of two parental VSG repertoires in a panel of cloned progeny by generating high quality contiguous assemblies of the two parental genomes by long read sequencing, chromatin-based assembly and optical mapping, with a focus on assembling the sub-telomeric regions and the VSG arrays. DNA of the 40 cloned progeny will be subjected to optical mapping, and the student will use this to analyse segregation of the parental VSG repertoires in progeny. The influence of sexual recombination upon the expression of VSGs during in vivo infections, including identifying that VSGs from both parental lines are expressed, reordering of hierarchical VSG expression, and ultimately immune escape, can then be tested.


1: Assembly of 2 parental genomes, incorporating long read, Hi-C and Bionano data, with a focus on subtelomeric regions and definition of VSG repertoires.

2: Generation of optical mapping data for 40 F1 progeny clones, and analysis of segregation of parental VSG repertoires.

3. Analysis of the influence of VSG segregation upon gene expression in progeny during in vivo infections.

Training Outcomes

The successful candidate will be trained in cutting edge bioinformatic genomic analysis, combining long read sequencing data, chromatin based assembly and optical mapping (Bionano) to analyse DNA, transcriptomic analysis of VSG expression, as well as molecular biology techniques, in vitro culture of trypanosomes and in vivo infections. This will result in cross-disciplinary abilities that provide a highly competitive platform for a future career in science.

This MRC programme is joint between the Universities of Edinburgh and Glasgow. You will be registered at the host institution of the primary supervisor detailed in your project selection.

All applications should be made via the University of Edinburgh, irrespective of project location. For those applying to a University of Glasgow project, your application along with any supporting documents will be shared with University of Glasgow.

Please note, you must apply to one of the projects and you must contact the primary supervisor prior to making your application. Additional information on the application process is available from the link above.

For more information about Precision Medicine visit:

Funding Notes

Start: September 2020

Qualifications criteria: Applicants applying for a MRC DTP in Precision Medicine studentship must have obtained, or will soon obtain, a first or upper-second class UK honours degree or equivalent non-UK qualification, in an appropriate science/technology area.
Residence criteria: The MRC DTP in Precision Medicine grant provides tuition fees and stipend of at least £15,009 (RCUK rate 2019/20) for UK and EU nationals that meet all required eligibility criteria.

Full eligibility details are available: View Website

Enquiries regarding programme:


1. Matthews et al, 2015. The within-host dynamics of African trypanosome infections. Philos Trans R Soc Lond B Biol Sci. 2015;370(1675).

2. Cooper et al, 2008. Genetic analysis of the human infective trypanosome Trypanosoma brucei gambiense: chromosomal segregation, crossing over, and the construction of a genetic map. Genome biology. 2008;9(6):R103.

3. Muller et al, 2018. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature. 2018;563(7729):121-5.

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