RP15: Investigating the plant mobilome responsiveness under stress

  • PhD Supervisor(s): Marie Mirouze & Alain Ghesquière
  • Host Institution: Institut de recherche pour le développement (IRD Diade), Monpellier, France
  • Duration: 36 months
  • Fixed start date: 1 April 2018
  • Planned secondment(s): IGA-TS (Udine, Italy) to receive training in TE-epiallele, MPG (Max Planck, Tübingen, Germany) for integration of sRNA with TE activity data.

Transposable elements (TEs) represent a main source of genomic diversity and an evolutionary force in plants. Host genomes have developed epigenetic mechanisms to control and prevent their proliferation. However, under specific stress conditions or at precise developmental stages, some TEs can be remobilized and proliferate in plant genomes. As TEs attract efficiently repressive epigenetic marks their mobility can have an impact on nearby gene regulation. In plants, only a few active TEs have been identified and the mobile part of the genome or mobilome, comprising these elements, is unknown. Notably the extent of TE mobility in plant populations in the wild is not known. To establish an unbiased repertoire of mobile TEs during plant development and in ecological conditions, we have developed the mobilome-seq as a simple strategy based on high throughput sequencing to detect TEs extrachromosomal forms (ecDNAs). It represents a novel approach to understand and evaluate the extent and impact of real time TE mobility on eukaryotic genomes.

In this project, the objectives are (1) to identify the full repertoire of mobile TEs through mobilome sequencing in stressed plants as compared to control plants, (2) to analyze the impact of identified TE mobility on genome stability and on epigenetic gene regulation. A pooled-individual mobilome-seq strategy will be used to identify treatment-specific ecDNAs. Subsequently, candidate mobile TEs detected by mobilome-seq will be screened using a sequence capture approach to evaluate neo-insertion sites. The impact of neo-insertions on gene regulation and epigenetic control will be assessed. We will compare the mobilomes of sexually and asexually reproducing wild Fragaria (strawberry) species, and of different Brassicaceae species that differ in life history characteristics (annual versus perennial) and habitat characteristics. On the same material, methylome and small RNA sequencing data will be made available by other groups from the EpiDiverse network and will be implemented in the analysis of TE candidates.

The PhD student will gain experience in computational analysis of genomic data and molecular biology (DNA extraction, ecDNA amplification, sequence capture).

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