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

Project Description

Royal (Dick) School of Veterinary Studies / The Roslin Institute

Background: The farming of finfish represents a critical global sector for current and future nutritional and economic security. In the UK, salmon farming is worth ~1.8 billion to the economy per annum, employs thousands, and represents the nation’s top food export. Disease is a pressing global 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, including by selective breeding and vaccine development. 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.

Novelty: The role of transcriptional diversity - generated by alternative splicing and transcriptional initiation - 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. Until recently, studying transcriptional diversity at the transcriptomic level was a challenge. However, long-read sequencing technologies have matured to a stage where full-length transcripts can be routinely sequenced. This project we will use Nanopore sequencing to capture full-length transcripts deployed by Atlantic salmon in response to different pathogen signals.

Main objectives:
1. Establish robust methods for full-length transcript sequencing in Atlantic salmon using Oxford Nanopore Technologies platforms. The student be trained in all steps, including RNA extraction and QC, Nanopore library preparation, sequencing of native RNA and cDNA, and downstream data processing and bioinformatics.
2. Establish transcript diversity deployed during antiviral and pro-inflammatory immune responses in Atlantic salmon. An in vivo and in vitro model will be used where either whole fish or primary immune cells cultures will be separately stimulated with pattern associated molecular patterns from bacteria and viruses. Nanopore sequencing will then be done for n=6 biological replicates at timepoints capturing the response dynamic.
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 founding members of an international initiative called FAASG (Macqueen et al. 2017), where understanding functional molecular diversity linked to disease resistance is a primary goal.
The PhD will feed important data into this coordinated effort.

Added value: The immune samples used in the PhD will be generated in H2020 project called ‘AQUA-FAANG’. High-resolution, matched functional genomics data, including extensive epigenomic marks, will be generated on the same samples, allowing findings on transcript diversity to be linked to a host of regulatory levels associated with gene expression.

Training opportunities: The student will gain training in molecular biology, functional and comparative genomics, bioinformatics, immunology, and molecular evolution. They will have opportunities to interact with the international salmonid genome biology community in collaborative projects.

All candidates should have or expect to have a minimum of an appropriate upper 2nd class degree. To qualify for full funding students must be UK or EU citizens who have been resident in the UK for 3 years prior to commencement.

Funding Notes

Completed application form along with your supporting documents should be sent to our PGR student team at

Please send the reference request form to two referees. Completed forms for University of Edinburgh, Royal (Dick) School of Veterinary Studies and the Roslin Institute project should be returned to by the closing date: 5th January 2020.

It is your responsibility to ensure that references are provided by the specified deadline.
Download application and reference forms via:
View Website


Macqueen DJ, et al. 2017. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics. 2017 Jun 27;18(1):484.
Houston RD, Macqueen DJ. 2019. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet. 2019 Feb;50(1):3-14

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