Functional role of transcript diversity in salmon immunity: development of full-length RNA sequencing

Disease is a pressing challenge to the sustainability of fish farming, causing huge economic loss, environmental issues, animal welfare problems, and reputational harm to industry. Consequently, there is a strong push for research to inform on mechanisms of disease resistance in fish. Such knowledge is needed to develop innovative solutions to reduce disease burden. In the proposed project, a novel approach will be taken to investigate a largely unexplored aspect of immune function in fish, which may have strong relevance as a mechanism of disease resistance.

The role of transcriptional diversity in fish immunity remains largely unexplored. Different transcript variants can encode distinct proteins or mRNAs with distinct translation potential and may be differentially deployed to impact host responses to pathogens. Long-read sequencing technologies have matured to a stage where full-length transcripts can be routinely sequenced. This project will use Nanopore sequencing to capture full-length transcripts deployed by Atlantic salmon in response to pathogen signals.

Main objectives:
1. Establish methods for full-length transcript sequencing in Atlantic salmon using Oxford Nanopore Technologies platforms.
2. Establish transcript diversity deployed during antiviral and pro-inflammatory immune responses in Atlantic salmon.
3. Identify transcript variants differentially expressed in response to pathogen signals and understand the impact of a salmonid-specific whole genome duplication event on the evolution of transcript diversity.
4. Improve the functional annotation of the Atlantic salmon genome. The supervisors are members of an international initiative called FAASG (Macqueen et al. 2017) where understanding molecular diversity linked to disease resistance is a primary goal.

The student will gain a thorough training in advanced molecular biology, functional and comparative genomics, bioinformatics, fish immunology, and molecular evolution. They will have extensive opportunities to interact with the international salmonid genome biology community in wider collaborative projects.

Other projects available:
We would encourage applicants to list up to three projects of interest (ranked 1st, 2nd and 3rd choice) from those listed with a closing date of 10th January 2020 at https://www.ed.ac.uk/roslin/work-study/opportunities/studentships