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

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.