Mots-Clés

Comparative genomics endosymbiosis genetic innovations

Description

Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Found in many different aquatic zones (marine and freshwater ecosystems, intertidal flats, soil, glacier and sea-ice…), these algae would be responsible for about 20% of the global carbon fixation and oxygen production on earth. Evolutionarily, diatoms are only distantly related to green algae and plants (Archaeplastida). Whilst these latter organisms are derived from the primary endosymbiosis of a cyanobacterium into an heterotrophic protist, diatoms and related organisms within the Stramenopila group, are derived from a secondary endosymbiosis, involving the capture of at least a red alga and green algae by another eukaryote (Falciatore et al., Plant Cell 2020).  Diatoms therefore display distinctive genomic, cellular and metabolic features compared to organisms of the green lineages and appear particularly suited from an evolutionary point of view to study the dynamics of intracellular genomes communication, and the genetic determinants of photosynthetic adaptation to different aquatic lifestyles.

This in silico project aims at shedding light on the genetics innovations of diatoms with regard to chloroplast functions, either in its biogenesis or in its metabolic activities. In the context of secondary endosymbiosis, paradigms established for Archaeplastida need to be revisited, in particular as regards (i) intracellular transport of proteins and metabolites between the cytosol and the chloroplast and (ii) the coordination of gene expression between the nucleo-cytosol and the chloroplast. Addressing these questions requires a comprehensive exploration and identification of chloroplast-targeted proteins or whose expression profile correlates with those of known chloroplast genes in diatoms. The focus will be made on genes possibly involved in the regulation of diatom chloroplast gene expression and those genes that are likely specific of the new genetic context of secondary endosymbiosis, among which should be a subclass that arose de novo in diatoms, i.e. from previously non-coding sequences.

For this aim, the post-doctoral associate will perform comparative genomics analysis to exploit the ~10 complete genomes of diatoms already published and additional genomic resources, soon available, from the 100 diatoms project consortium, from which the host lab is a member. He/she also will have access to transcriptomics and proteomics data and resources generated in the host laboratory (e.g, DiatOmicBase platform to mine diatom omics data) and publicly available data such as the MMETSP- Marine Microbial Eukaryote Transcriptome Sequencing Project (Keeling et al. Plos Biol 2014) and metadata of the Tara Ocean project (Carradec et al., Nat comm. 2018).

Requirements:

- PhD or previous post-doc in the field of comparative/evolutionary genomics

- Skills/experience in phylogenomics, molecular evolution, evolution of gene repertoires

- Strong skills in programming and statistics

- Excellent abilities in data analyses, writing of scientific papers, communication, teamwork.

Location: the position is available for 24 months with a flexible start between January and March 2023, in the heart of Paris at Institut de Biologie Physico-Chimique, in the team Evolution of Photosynthetic Functions and Genome Dynamics in Microalgae of the Laboratory of Chloroplast Biology and Light-sensing in Microalgae http://www.ibpc.fr/UMR7141. The post-doctoral associate will benefit from the environment of experts in sequence analysis and genome evolution, diatoms biology and functional genomics, chloroplast biology and photosynthesis, which should allow him/her to imagine and design new experiments as she/he progresses in this research project.

For more details of the context, contact Ingrid Lafontaine (ingrid.lafontaine _at_ ibpc . fr )