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PhD on dietary adaptations in ant-eating mammal genomes and microbiomes (M/F)

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Français - Anglais

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General information

Reference : UMR5554-FREDEL-004
Workplace : MONTPELLIER
Date of publication : Monday, July 27, 2020
Scientific Responsible name : Frédéric Delsuc
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2020
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Missions:
As part of the ERC Consolidator ConvergeAnt project (www.convergeant-project.com/), we are looking for a PhD student with experience in transcriptomic and genomic data analysis and microbiome characterization. The overall objective of the project is to study the mechanisms underlying the evolutionary convergence among independent lineages of myrmecophagous mammals (feeding mainly on ants and termites). The project proposes an integrative approach to answer this question by combining the study of the morphology, genome, and microbiome of these different species. The PhD project is divided in two parts: a first part focusing on the characterization of genomic adaptations in relation to the myrmecophagous diet and a second part exploring the potential role of the microbiome in the digestion of social insects. The genomic part will exploit the genomes and transcriptomes already sequenced to reconstruct the evolutionary history of three gene families potentially related to the myrmecophagous diet: mucins (MUCs), taste receptors (TASRs), and olfactory receptors (ORs). The metagenomic part will focus on the reconstruction of complete bacterial genomes from faecal samples already available for the analysis of chitin degradation pathways in the intestinal microbiome of myrmecophagous species. The candidate will be in charge of the production of molecular data for the microbiome part of the project in coordination with the research assistant in charge of the laboratory by metagenomic long read sequencing (Nanopore).

Activities:
- Field work: Possibility to participate in sample collection missions and portable field DNA sequencing in French Guiana and South Africa.
- Sequencing: Coordination of sequencing projects in interaction with the different people and sequencing platforms involved in the project. Implementation of field metagenomic sequencing using the MinION portable device.
- Analyses: Assembly and functional annotation of metagenomic data, characterization of metabolic pathways by bioinformatics analysis.
- Publications: Writing scientific articles and participating in international meetings.

Requirements:
- Experience in assembling and annotating complete genomes from metagenomic data (Illumina and Nanopore).
- Experience with statistical analysis of comparative genomic and transcriptomic data.
- Fluency in scientific, oral and written English.
- Ability to work autonomously and rigorously.
- Capacity for integration and teamwork.

Work Context

The ConvergeAnt ERC project is led by Frédéric Delsuc (http://fdelsuc.wixsite.com/homepage) of the Phylogénie et Evolution Moléculaire team at the Institut des Sciences de l'Evolution (ISEM) UMR 5554 CNRS-UM-IRD-EPHE (http://www.isem.univ-montp2.fr/), located on the University of Montpellier campus. This integrative project is the subject of regular meetings with the other people involved in the laboratory in which the candidate must participate.

Constraints and risks

Not applicable

Additional Information

For additional informations please contact
Frédéric Delsuc (Frederic.Delsuc@umontpellier.fr).

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