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PhD Thesis (M/F) "Genomics of snow algae: life in the snow, from the genome to the cell and to populations"

This offer is available in the following languages:
Français - Anglais

Date Limite Candidature : jeudi 2 juin 2022

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General information

Reference : UMR5168-ERIMAR-003
Workplace : GRENOBLE
Date of publication : Thursday, April 28, 2022
Scientific Responsible name : Eric Maréchal
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

We are looking for a candidate for a thesis entitled "Genomics of snow algae: life in the snow, from the genome to the cell and to populations". This thesis is part of the CNRS "80 Prime" program of excellence. The candidate should have a strong background in bioinformatics, with a high degree of autonomy, to manipulate genomic data (assembly, annotation, genome comparisons, etc.) and analyse metagenomic data. The candidate should have an interest in the study of microorganisms in their ecosystems and adaptive processes, in a context of environmental change related to global warming. He/she will develop his/her work mainly through in silico approaches, in contact with colleagues developing experimental aspects. He/she should therefore be both autonomous and comfortable in a multidisciplinary team context. Subject description: The snow above the tree line is populated by unicellular organisms of which very few species have been described, and no genome characterized. The pioneer forms are photosynthetic microalgae, some of which can become dominant, accumulating carotenoids and coloring the snow red. In the framework of the Alpalga program (https://alpalga.fr/?lang=en), sampling campaigns by the laboratories proposing this project, in the Alpine Workshop Zone carried out from 2017 to 2022 have allowed the purification of different species: 4 cultivable algal genomes have been sequenced, 1 non-cultivable algal genome is being sequenced from metagenomic data and 1 unicellular snow fungus is also being sequenced. With these unique data, the thesis project aims at the first genomic characterization of eukaryotic microorganisms inhabiting snow, from the molecular and cellular levels (functional genomics), to the population and longer term community levels (environmental genomics), in order to decipher what it means to "live in the snow".
The project will rely on the student's significant expertise in bioinformatics/genome analysis (annotation, genome comparison, metagenomics), requiring access to original genomics data. Most of these data are already available. The project therefore combines a low-risk, or even no-risk, part of annotation and comparative genomics, and a more exploratory part aimed at understanding the structuring of populations in space and time. For this second part, the risk will be controlled by focusing on a reasonable number of species, characteristic of the environments explored.

Work Context

The thesis will take place in two research institutes in Grenoble. First, the thesis will take place at the LPCV (Cell and Plant Physiology Lab), a laboratory expert in the culture and manipulation of microalgae, studying these organisms from the molecular level (genes) to the cellular level. The LPCV is composed of about 100 people. It has microalgae culture facilities, and all the technical means to extract and sequence their genomes, characterize their physiological state and transcriptomic and lipidomic profiles. See https://www.lpcv.fr/Pages/Lipid/Presentation.aspx for more information on the LIPID team. In a second phase, the thesis will be pursued at the LECA (Alpine Ecology Laboratory), a reference laboratory for the study of environmental DNA. The thesis will benefit from original genomic data already produced in the framework of the Alpalga program (https://alpalga.fr/?lang=en), or in the process of being produced, and will explore these data with the help of bioinformatics approaches mastered by both units, to contribute to the identification of potential adaptation mechanisms to life in the snow, and to explore the structuring of the corresponding populations in the natural environment and their dynamics.

Constraints and risks

The project does not present any particular risk exposure.

Additional Information

We are looking for a candidate for a thesis entitled "Genomics of snow algae: life in the snow, from the genome to the cell and to populations". This thesis is part of the CNRS "80 Prime" program of excellence. The candidate should have a strong background in bioinformatics, with a high degree of autonomy, to manipulate genomic data (assembly, annotation, genome comparisons, etc.) and analyse metagenomic data. The candidate should have an interest in the study of microorganisms in their ecosystems and adaptive processes, in a context of environmental change related to global warming. He/she will develop his/her work mainly through in silico approaches, in contact with colleagues developing experimental aspects. He/she should therefore be both autonomous and comfortable in a multidisciplinary team context. The thesis will take place in two research units, the Cell and Plant Physiology Lab (LPCV) and in a second time the Alpine Ecology Lab (LECA). Brief description of the subject: The snow above the tree line is populated by unicellular organisms of which very few species have been described, and no genome characterized. The pioneer forms are photosynthetic microalgae, some of which can become dominant, accumulating carotenoids and staining the snow red. In the framework of the Alpalga program (https://alpalga.fr/?lang=en), collections made by the laboratories proposing this project, in the Alpine Workshop Zone carried out from 2017 to 2022 have allowed the purification of different species: 4 cultivable algal genomes have been sequenced, 1 non-cultivable algal genome is being sequenced from metagenomic data and 1 unicellular snow fungus is also being sequenced. Thanks to these unique data, the thesis project aims at the first genomic characterization of eukaryotic microorganisms inhabiting snow, from the molecular and cellular levels (functional genomics), to the population and longer term community levels (environmental genomics), in order to decipher what it means to "live in the snow".

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