Créé(e) 05/02/2021 Mis à jour 20/09/2021

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A post doc position in bioinformatics is opened in DYDIV team (DYnamics of the marine DIversity)

Funded two years Postdoctoral position available

Transposable elements (TEs) are major factors of genome plasticity involved in many evolutionary and ecological processes such as stress response, adaptation and colonization mechanisms. Parasite attack is one of the main biotic factors that can activate TEs, but examples remain marginal in animals as well as possible exchanges of genetic material by horizontal transfer between the parasite and the host. Bivalves offer a perfect opportunity for this. At least 7 genomes have already been sequenced, and for species of economic interest, numerous data are available. This is particularly the case for two species whose parasites can induce high mortality during farming: (i) the flat oyster Ostrea edulis (infected by Marteilia refringens and Bonamia ostreae); (ii) the American clam Mercenaria mercenaria (infected by QPx). The genomes of these 2 species and their parasites have recently been assembled with good quality. The flat oyster has recently been the subject of a project to promote sustainable and viable management of fishery resources. Several biparental lines have been produced and exposed to different environments (especially for parasitoids) in natural conditions, in order to select them for hardiness, resistance and growth with genetic markers.

The main objective of the new project is to strengthen this theme by developing a complementary component on the potential role of ETs. The aim of the study is to analyze the diversity of the elements and to see how they can react in different environmental contexts and more particularly if they can be used as biomarkers for parasitic attacks in natural environments, and have a genomic impact that has favored the adaptation of families. The results obtained on the ETs will then be compared to data obtained elsewhere on other types of molecular markers (SNPs). The candidate will have to establish the patterns of diversity in ETs and various genome components in the diverse bivalve genomes available and thus participate in the fine annotation of our 5 assembled genomes (flat oyster, clam and their parasites). It will then be possible to follow the differences in expression of these ETs and others genes under different environmental conditions and especially for different levels of infection. The second objective will be a comparative genomics study of the ETs to look for possible variations in their insertions between selected populations or families according to the environment, physiology (growth) and health status of the host.

The candidate should have a strong background in bioinformatics with good knowledge of programming (python, biopython,..), sequence analysis, and of evolutionary genetics / genomics. He/she should have a strong interest in evolution and adaptation issues. Practical knowledge in comparative genomics and/or differential display will be appreciated. Although this may be a plus, it is not essential to have a strong knowledge of transposable elements, if needed a refresher on theoretical and practical aspects can be provided in the laboratory.

The post-doc will carry out his research in the new team "Dynamics of Marine Diversity", at the ‘Station Biologique de Roscoff’ (Sorbonne University-CNRS), Roscoff, where we are part of a larger oceanography research community. And a close collaboration will be set up with  A. Tanguy (SBR) and J. Filée (EGCE, Gif sur Yvette).

We are looking for motivated post-doctoral candidate who, as a reminder, must have spent at least 18 months outside France between May 1, 2017 and the start of the project’; must begin no later than July 1, 2022 (which implies to have all the administrative documents completed in April); and who must not have completed more than 2 years of post-doctoral internship at the beginning of the contract.

Letters of intention (CV, declaration of research interests, previous experience and fit for the position, email address of potential contacts for reference letters) should be forwarded to:

Eric Bonnivard (

UMR Sorbonne-Université-CNRS 7144
Equipe DYDIV
Dynamique de la diversité marine
Station Biologique de Roscoff
Place Georges Teissier
CS 90074
29688, Roscoff cedex

Tel : +33(0)2 98 29 25 27

The review of applications starts on October, 2021, and will continue until the position is filled.


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