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PhD in genomics to study horizontal transfers in plants and other organisms (M/F)

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : lundi 11 juillet 2022

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General information

Reference : UMR5096-MOAELB-001
Workplace : PERPIGNAN
Date of publication : Monday, June 20, 2022
Scientific Responsible name : Moaine El Baidouri
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Horizontal transfer (HT) refers to the movement of genetic material between distant species by mechanisms other than sexual reproduction. In prokaryotes, horizontal transfers are well known to be a source of novel adaptive traits, such as the spread of genes involved in antibiotic resistance. Over the past decade, it has become increasingly clear that in eukaryotes as well, such as plants, HTs can also lead to major evolutionary leaps and very rapid adaptation to new ecological niches that would not be possible through standard genetic mutations alone. However, little is known about the biotic interactions promoting HTs between plants and the possible involvement of vectors in these HTs between plants. In previous work conducted on 40 plant species, we identified more than 32 transposable element (TE) HTs between 26 distantly related plants (El Baidouri et al 2014). This study was the first demonstration that HTs are far from anecdotal and that host-parasite interactions may not be the only pathway for these frequent interspecies genetic exchanges. With the advent of new and third generation sequencing technologies and the substantial increase in genomic data in plants, it is becoming possible to assess HT pathways on a large scale. In this project, we will use new innovative bioinformatics tools recently developed in our lab that aim to characterize HTs at the whole genome level and without any prior knowledge of genome annotation. With these tools, we will characterize plant-to-plant and plant-to-other organisms HTs (fungi, insects, bacteria, virus) at an unprecedented scale by comparing thousands of genomes. This will lay the foundation for a better understanding of HTs routes and to determine the nature of biotic relationships that promote them as well as the involvement of intermediate vectors in plant-to-plant transfers.

Profile and skills required

The successful candidate should have a Master's degree in plant biology or bioinformatics and have strong experience in the analysis of large sequencing datasets, comparative genomics and be familiar with the LINUX environment. The candidate must have good writing skills and a good command of spoken and written English. Knowledge of one of the following programming languages: Bash/Python/Perl or R would be an asset.

Work Context

This PhD will be carried out at the Plant Genome and Development Laboratory (LGDP), located in Perpignan under the supervision of Moaine El Baidouri. The LGDP studies the dynamics of the plant genome and the regulation of gene expression, particularly during development, acclimation and adaptation to abiotic stresses.

Additional Information

PhD with secured funding (ANRJCJC project)

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