PhD position OT-22239

PhD : Single-cell analysis of endoreduplicated cells from tomato fruit


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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

We are looking for a candidate with knowledge in plant development and/or tissue/cell growth, preferably with experience in transcriptomic data analysis, for a fully-funded three-year PhD position as part of the ANR TomENDCODE project. The project focuses on single-cell RNA sequencing analysis of polyploid nuclei populations from tomato fruit. These polyploid cells result from the endoreduplication process, where DNA is replicated without cell division, which is associated with cell and tomato fruit growth. The project aims to elucidate the trajectory of these cells during endoreduplication and the underlying mechanisms regulating gene expression.

More specifically, you will be in charge of:

  • Monitoring tomato plants in the greenhouse and collecting samples for omics analyses.
  • Performing flow cytometry analysis and nuclei sorting.
  • Preparing and conducting single-cell RNA-seq experiments, in situ hybridization, and spatial transcriptomics analyses.
  • Performing bioinformatic analysis of sequencing data and integration of omics data.
  • Conducting confocal microscopy experiments and genome editing using CRISPR-Cas9.
  • Responsible for setting up experiments, collecting and analyzing data, and presenting findings in the form of posters, conferences, and scientific publications.

You will join the FDFE team (Fruit Development, Flowering, and Environmental constraints) at the Fruit Biology and Pathology Laboratory, located on the Villenave d’Ornon campus of the INRAE Bordeaux-Nouvelle Aquitaine centre. You will have access to facilities such as greenhouses and imaging platforms on this campus, as well as neighbouring laboratories with single-cell and genomic platforms. The team specializes in fruit growth, endoreduplication, genomics, bioinformatics, biotechnology, and imaging. You will work in a stimulating environment within a campus that hosts several leading research laboratories focused on plant sciences, plant pathology, and environmental sciences, with state-of-the-art facilities for plant growth, metabolomics, and imaging. Flow cytometry and genomic platforms are also conveniently located at the University of Bordeaux and INRAE Pierroton sites, less than 15 minutes from the laboratory. You will benefit from the scientific expertise of your supervisors, Nathalie Gonzalez and Pascal Martin, and the FDFE team members in plant growth, endoreduplication, cell biology, functional genomics, imaging, and bioinformatics.

Special working conditions: Frequent travel to local platforms (~15 minutes away).

A driver's license is required.

Training and skills

Master's degree/Engineering degree

Recommended training: Master degree in Plant Science, Biotechnology, Molecular and Cellular Biology, or Bioinformatics (with a background in Biology), Agricultural Engineer with a specialization that includes laboratory work.

Knowledge required: A strong background in molecular biology and genomics, preferably with substantial experience in omics approaches. Basic knowledge in bioinformatics and an understanding of statistical analysis.

Appreciated experience: Experience in bioinformatics and using the command line, a strong interest in developmental biology, experience in microscopy.

Skills sought : Motivation and interest in developing expertise that includes both large-scale omics data production and their bioinformatics analysis and integration. Good communication skills, including in written and spoken English. Rigor and organization. Keen to collaborate with colleagues from different scientific backgrounds (biologists, bioinformaticians).

INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
parenting support: CESU childcare, leisure services;
- skills development systems: trainingcareer advise;
social support: advice and listening, social assistance and loans;
holiday and leisure services: holiday vouchers, accommodation at preferential rates;
sports and cultural activities;
- collective catering;

- financial contribution for home/work subscription (Bus, tram).

How to apply

I send my CV and my motivation letter

All persons employed by or hosted at INRAE, a public research establishment, are subject to its internal regulations, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear.  

Offer reference

  • Contract: PhD position
  • Duration: 36 months
  • Beginning: 01/10/2024
  • Remuneration: 2 100 euros gross
  • Reference: OT-22239
  • Deadline: 30/08/2024
Centre Nouvelle-Aquitaine Bordeaux

Biologie et Pathologie du Fruit 33140 VILLENAVE D'ORNON Website


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