Mots-Clés

population genomics long reads parasites

Description

18-month postdoc position in population genomics of an emerging plant parasitic nematode

We are looking for a highly motivated postdoc to work on the population genomics of the emerging plant parasitic nematode Meloidogyne enterolobii as part of the AEGONE project.

AEGONE (for Adaptability, Origin and Genome Evolution of an emerging plant-devastating nematode) is co-funded by ANR in France and DFG in Germany. This project is a collaborative effort between Institut Sophia Agrobiotech (ISA) in France and the Julius Kühn-Institut (JKI) in Germany. ISA, which is the hosting lab, is a leader in root-knot nematode genomics and was the coordinator of the first genome sequencing project for a plant parasitic animal. The associated lab, JKI was the first to discover and describe the root-knot nematode Meloidogyne enterolobii in Europe and hosts a unique collection of populations for this species.

Main goals

We aim at studying the relationship between genome variations and phenotypic variations as well as adaptability in the emerging root-knot nematode M. enterolobii.

The postdoc will mainly have to identify and describe genome variations in this species using highly accurate long reads (PacBio Hi-Fi) for 10 populations. This will include:

• SNP and short indels
• Structural Variations (insertions, deletions, inversions, translocations, copy number variations)

The 10 M. enterolobii populations will then be genotyped using the variations discovered and compared to each other to evaluate their relatedness and distance at the whole-genome level.

Experiments already performed at JKI on these 10 M. enterolobii populations allowed demonstrating they show phenotypic variations in terms of virulence and ability of parasitize 20 monitored crop plants.

The next steps of the project will consists in monitoring whether some genome – phenome co-variations can be identified in this species.

Skills

The candidate must:

• be skilled in comparative and population genomics
• have good experience in writing papers and communicating research in conferences
• be familiar with Linux working environment
• have a taste for teamwork

Work environment

This part of the project will take place in the Genomics & Adaptive Molecular Evolution (GAME) team at Institut Sophia Agrobiotech (ISA) in the French Riviera. GAME is a young and international team mainly using bioinformatics and biostatistics to study adaptive genome evolution in various species interacting negatively or positively with plant health. ISA combines scientists and facilities from INRAE, Université Côte d’Azur and the CNRS. This project will benefit from the support of ISA bioinformatics & genomics (BIG) platform with local skills in bioinformatics, computational power and storage available.

When

The position is available immediately and must start no later than the 30th of June 2022

Salary

Gross monthly salary will be between 2,800 -3,000 € depending in experience and qualifications.

How to apply

Send an e-mail to etienne.danchin[@]inrae.fr and attach a CV and motivation letter. Do not hesitate to use the same address to inquire about the position.