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The role of retrotransposon mobilization in forest trees genome adaptation.

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  • Full or part time
    Dr M Catoni
    Dr E Luna-Diez
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Environmental changes and biotic stresses are powerful drivers of evolutional adaptation. However, the main contributors to genome plasticity are yet not fully characterized. Retrotransposons are genetic elements able to copy their DNA sequence and integrate in a new chromosomal location. Therefore, retrotransposons play a critical role in genome plasticity, adaptation and evolution.
Once activated, retrotransposons can multiply in a similar way to viruses and populate the genome of the host organism. They are particularly abundant in plants, and contribute to a large portion of genomes (e.g. 42% of apple tree genome, while coding genes account for only 23%). In spite of their selfish behaviour and potential mutagenic activity, retrotransposons mobilization directly impact many plant traits. However, the detection of potentially active retrotransposons is challenging because i) their mobilization is difficult to be observed and it is not necessarily associated to a phenotype and ii) retrotransposon activation is restricted in time (developmental stage) and space (tissue/organ) by multiple mechanisms. Therefore, their activity cannot be easily predicted.
The application of genome wide approaches have facilitated the discovery of active retrotransposons in plant species with small genome and well-assembled references (e.g. Arabidopsis, rice). However, in plants with larger and yet uncharacterized genomes the retrotransposons activity is strongly underestimated. To fill this gap, with the proposed project we aim to screen for active retrotransposons in forest trees, to characterize their expression and mobilization, and to study their impact on genome adaptation to environmental changes and stress.
The selected student will apply ground-breaking newly established methods for efficient detection of active retrotransposons, independently of the availability of an annotated reference genome. These procedures are based of the direct detection of intermediates retrotransposons copies, before their integration in the genome. The new retrotransposons identified will be sequenced, and their activation and mobilization will be studied in relation to environmental stresses, including pathogen infections, global warming and increase atmospheric CO2 concentration. With this project, we will identify retrotransposons active in natural conditions, and their potential contribution to genome evolution in a natural environment.
The material for the initial screening will be collected from different tissues of trees growing at BIFoR-FACE facility (Oak, Hazel, Hollytree, Sycamore and Hawthorn). These species have very limited genomic information but potential high content of uncharacterized retrotransposons in their genome. The retrotransposon screening will be performed with new methods developed for specific amplification and sequencing of extrachromosomal DNA, a molecule produced during retrotransposon mobilization. Once the DNA of new element is known, classic molecular biology methods will be used to study their transcriptional activity, mobilization patter and epigenetic regulation.

Funding Notes

Full payment of tuition fees at Research Councils UK fee level for year of entry (£4,270 in 2018/19), to be paid by the University;
An annual maintenance grant at current UK Research Councils rates (national minimum doctoral stipend for 2018/19 is £14,764), to be paid in monthly instalments to the Leverhulme Trust Doctoral Scholar by the University.
All studentships will come with a minimum of £3,000 Research Training Support Grant. This can be increased up to a maximum of £12,000. Supervisors should indicate from where any further costs necessary for the project will be sourced.


Lisch, D. (2013). How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61.
Griffiths, J., Catoni, M., Iwasaki, M., and Paszkowski, J. (2018). Sequence-Independent Identification of Active LTR Retrotransposons in Arabidopsis. Mol. Plant 11, 508–511.
Lanciano, S., Carpentier, M.C., Lauro, C., Jobet, E., Robakowska-Hyzorek, D., Lasserre, E., Ghesquière, A., Panaud, O., and Mirouze, M. (2017). Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLOS Genet. 13, e1006630.
Cho, J., Benoit, M., Catoni, M., Drost, H.G., Brestovitsky, A., Oosterbeek, M., and Paszkowski, J. (2018). Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants. BioRxiv. doi:

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