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  Dr M Saitou  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

About the position

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).

Main tasks

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.

Remuneration and further information

The position is placed in government pay scale position code 1017 PhD. Fellow. PhD. Fellows are normally placed in pay grade 54 (NOK 482.200,-) on the Norwegian Government salary scale upon employment and follow ordinary meriting regulations.

Employment is conducted according to national guidelines for University and Technical College PhD scholars.

For further information, please contact Dr. Marie Saitou (Principal Investigator)

Website: https://sites.google.com/view/saitou-lab

Information for PhD applicants and general information to applicants

Application

To apply online for this vacancy, please click on the 'Apply for this job' button of the JobbNorge page This will route you to the University's Web Recruitment System, where you will need to register an account and log in before completing the online application form.

Application deadline: July the 11th 2022

Applications should include (electronically)

  • One page A4 letter of intent, including
  • Q1, Why are you interested in this project?
  • Q2, How can you contribute to the project based on what you have learned so far?
  • Curriculum vitae with a publication list
  • Certified copies of academic diplomas and certificates. (i.e. Di-ploma, transcript. Diploma supplement for both bachelor and master). Diplomas, transcripts and diploma supplements that are not in Norwegian or English must be uploaded in the original lan-guage. An English translation of these documents must also be at-tached.
  • Applicants from universities outside Norway are kindly request-ed to send a diploma supplement, or a similar document, which describes in detail the study program and grading system.
  • Names and contact details of three references
  • Documentation of proficiency in written and oral English

References

[1] Lien, et al., https://doi.org/10.1038/nature17164
[2]Bertolotti, et al., https://doi.org/10.1038/s41467-020-18972-x
[3] Stenlokk, et al., (in press, will be published in June) https://dx.doi.org/10.1098/rstb.2021.0195
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