Mots-Clés

Comparative genomics, Microbiome analysis, Genome-Environmental-Analysis

Description

Background

The evolutionary pathway underlying interactions between hosts and their microbiome is a black box on which biologists have long attempted to shed light. A limiting factor has been knowledge of the precise molecular events, which are now increasingly possible to elucidate with the advent of next-generation sequencing technologies. Coupled to these technologies experimental evolution can help in elucidating on the evolutionary changes occurring in complex biotic interactions. In this context, the ERC project HoloE2Plant will validate the holobiont concept by looking at the simultaneous evolution of the host and its microbiome. This will be possible thanks to an experimental coevolution approach applied to fast-cycling Brassica rapa plants and Synthetic Microbial Communities (SynComs).

Concerning the work environment, the IGEPP laboratory at Rennes is a multidisciplinary workplace including research teams working on plant genomics/genetics, ecology, evolution and agronomy. We have a new plant care platform and a culturomics and molecular biology high-tech laboratory. English and French are the two official languages in the laboratory. We dispose of weekly scientific seminars and team meetings. The laboratory is located approximately 20km from Rennes and is accessible by transports.

Specific Activities

• Analysis of NGS data obtained thought metabarcoding approaches (gyrB and ITS sequencing for describing bacterial and fungal communities respectively). In this context the bioinformatician will demultiplex the NGS data and use MOTHUR and or DADA2 to reconstruct OTUs matrices.
• Use of the OTUs matrices to estimate the alpha- and beta-diversity of both fungal and bacterial communities
• Analysis of a large microbial collection characterized through gyrB and ITS sequencing. The bioinformatician will BLAST sequences obtained from the microbial collection with those extracted from the metabarcoding analysis to identify possible matches
• Genome mapping of Brassica rapa genomes obtained by Illumina sequencing and reconstruction of allele frequency matrices for the calculation of Fst. Utilization of the plant allele frequencies to run Genome-Environmental-Analysis (GEA) with the ByPass Bayesian method to identify plant loci interacting with microbial descriptors estimated from the metabarcoding and microbial collection data.
• Use the B. rapa genomes to extract bacterial and fungal sequences by Kraken, a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Reconstruct the microbial genomes from the sequences trimmed by Kraken and run the GEA on this dataset

Requested skills

We are looking for applicants with a strong academic background who have completed a five-year master degree (3+2) (or equivalent according to NARIC) in Bioinformatics and Genome Analysis. The bioinformatician should demonstrate to have NGS and genome analysis, statistics and programming in R, Python or Perl is mandatory for this position. The ability to manage large genomic dataset is also mandatory. English or French are the languages used in the research team.

How to apply

Applications should be provided in a single pdf document at the following address: claudia.bartoli-kautsky@inrae.fr. The pdf should include: i) a motivation letter explaining your interest in the project and the relevance of your background and experience ii) a CV with a full summary of your education and experience iii) diplomas certifying you are eligible and iv) 2 recommendation letters.

The INRAE Institute is an equal opportunities employer, actively supporting inclusivity and diversity. We offer an exciting, stimulating, diverse research environment and a friendly workplace. We obtained in 2020 the Afnor label « Alliance ». We respect the 25 diversity and equality criteria https://www.inrae.fr/actualites/diversite-egalite-professionnelle-double-labellisation-afnor-etendue-lensemble-linstitut