The Department of Animal and Aquacultural Sciences, Faculty of Biosciences at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year Ph.D.–position in evolutionary genomics. The position is financed by the RCN-funded project SalmoSV and linked to FHF-funded project SynchroSmolt. The projects seek to understand the genome evolution and phenotype-affecting variants following a recent whole-genome duplication of Atlantic salmon.
Genomic structural variants including deletions, duplications, inversions, and translocations of genetic sequences, are rich resources for genetic diversity. In particular, Atlantic salmon genomes show extreme levels of genomic structural variants, likely due to their unique history of recent whole-genome duplication. Structural variants in Atlantic salmon genomes are one of the most promising frontiers in both evolutionary genomics and aquacultural genomics. However, due to their complex nature, which and how structural variants have driven adaptive evolution with functional advantage are yet to be clarified. Long-read sequencing is a cutting-edge technique to identify previously undiscovered structural variants. In our ongoing project, the genomic map of Atlantic salmon with long-read sequences is getting ready for deep investigation.
The goal of this project is to reveal adaptive structural variants have driven and their functional advantages by integrating omics data sets. The Ph.D. project will focus on the estimation of the effects of structural variants on various phenotypes bioinformatically. The other focus of this Ph.D. project is to reveal the adaptive evolution of structural variants of farmed salmon under domestication compared to their wild counterparts. The candidate will work in close collaboration with other Ph.D. students, postdoctoral researchers, and senior researchers.
The successful candidate will join CIGENE (https://cigene.no/), a multidisciplinary genome biology research group. CIGENE has established excellent wet lab facilities (CIGENE genomics lab) for automated high-throughput omics analyses and gene-editing technology, as well as the connected CIGENE Bioinformatics & Computational Unit with IT specialists to support the transfer, storage and analysis of omics data, currently administering a computer cluster. The unit will make use of both our local computer cluster with 580 CPUs, 4TB RAM and 600TB storage and national computational resources (NOTUR/Sigma2 and NORSTORE).
The main goal of this project is to reveal the adaptive evolution and functional effect of structural variants in Atlantic salmon. The main tasks are bioinformatic analyses of publicly available genomics and transcriptomics dataset in the view of evolution.
Specifically:
Literature review to explore relevant studies and methods
Estimate the effect of genomic structural variants on smoltification, the physiological “metamorphose” from fresh water to seawater in Atlantic salmon.
Compare population-scale genomes of geographically broadly distributed wild Atlantic salmon and farmed Atlantic salmon and identify adaptive genomic evolution.
Extend the evolutionary analysis at the cross-species scale and reveal the deeper evolutionary history of target genes.
Publish three peer-reviewed papers under the supervision of advisors
The successful candidate is expected to enter a plan for the progress of the work towards a Ph.D. degree during the first months of the appointment, with a view to completing a doctorate within the Ph.D. scholarship period. Presentation of findings at international conferences or/and attending international workshops/visiting relevant researchers are highly encouraged and financially supported.
Competence
The successful applicant must meet the conditions defined for admission to a PhD programme at NMBU. The applicant must have an academically relevant education corresponding to a five-year Norwegian degree programme, where 120 credits are at master's degree level. The applicant must have a documented strong academic background from previous studies and be able to document proficiency in both written and oral English. For more detailed information on the admission criteria please see the PhD Regulations and the relevant PhD programme description.
The applicant must document expertise and interest in the research subject.
Required qualifications:
Master’s degree in genomics, bioinformatics, evolutionary genetics, or a similar field.
The following experiences and skills will be emphasized:
Experience with genome data analysis
Experience with command-line-based operation, R/python
Experience with the High-Performance Computing (HPC) system
Experience with relevant technologies and lab techniques
You need to:
Have strong communicative and interpersonal skills
Be a highly motivated team-player who is committed to being a part of a positive, collaborative, and supportive research group
Be proficient in English, both written and spoken
Have solid analytical skills and an academic approach to research questions.
The Norwegian University of Life Sciences (NMBU) has a particular responsibility for research and education that secures the basis for the life of future generations. Sustainability is rooted in everything we do and we deliver knowledge for life. NMBU has 1,800 employees of which about 250 phd scholarships and 6,000 students. The university is divided into seven faculties and has campuses in Ås and Oslo. We will be co-located in Ås from 2021.
NMBU believes that a good working environment is characterised by diversity.
We encourage qualified candidates to apply regardless of gender, functional ability, cultural background or whether you have been outside the labour market for a period. If necessary, workplace adaptations will be made for persons with disabilities.
