About the Project
The studentship aims to define the role of transposable elements (TEs) as agents for adaptive evolution following whole genome duplication (WGD), focussing on early stages of development. The project will exploit salmonid fishes as an ideal study system, due to the presence of an ancestral WGD event that re-shaped genome evolution and has been positively linked with lineage diversification (e.g. Lien et al. 2016; Robertson et al. 2017).
The student will test the hypothesis that TEs have been instrumental agents in reshaping genome sequence and epigenetic evolution post-WGD, promoting lineage-specific developmental programmes. The project will involve comparative analysis of salmonid species and an outgroup lineage that did not experience WGD, investigating several layers of functional regulation (see Macqueen et al. 2017) including transcriptomics to characterize genome-wide expression changes in duplicated genes. Gene expression data will be linked to TE sequence evolution and changes in epigenetic status. The analyses will focus around early developmental stages including embryogenesis.
Additional information : This PhD is embedded within a Norwegian research project called TRANSPOSE: Transposable elements as agents of genome evolution and adaptation following a recent whole genome duplication. The student will benefit from extensive interactions with a world-leading network of salmonid researchers involved in TRANSPOSE, including close links with scientists based at the Norwegian University of Life Sciences that helped deliver the Atlantic salmon genome (Lien et al. 2016).
Training opportunities : The student will be trained to apply leading-edge genomics technologies including RNA-seq and ATAC-seq, and deal with omics datasets using advanced bioinformatic tools. They will receive training in fish development, molecular biology, comparative analysis, evolutionary genomics and phylogenomics.
The candidate: we are seeking a strong student with interests and preferably experience in any of the following fields: bioinformatics, genomics, development and evolution. The successful candidate will have at least an upper 2:1 degree in the biological sciences (or a closely-related field) and preference will be given to individuals with a Masters degree relevant to the project, or other first-hand experience in bioinformatics and genomics. The successful student will be required to travel outside the UK for fish sampling, potentially for extended periods.
Other background : Dr Macqueen is in the process of making a move from the University of Aberdeen to the Roslin Institute (University of Edinburgh). This PhD vacancy was previously advertised at the University of Aberdeen, but will now run from the Roslin Institute with a delay of two months from the original intended start date, hence this new advertisement. Candidates that applied through Aberdeen have been contacted already.
Application procedures:
Applications including a statement of interest and full CV with names and addresses (including email addresses) of two academic referees, should be emailed to [Email Address Removed]. When applying for the studentship please state clearly the title of the studentship and the supervisor/s in your covering letter.
References
Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Vge DI, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. 533, 200-5.
Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escrate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, lafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE, Rise MR, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yez JM (The FAASG Consortium) (2017) Functional Analysis of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics. 18: 484.
Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PW, Sandve SR, Macqueen DJ (2017) Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18: 111.
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