Place Georges Teissier
Background: Ectocarpus subulatus is a highly stress-tolerant species of brown frequently found in environments with high temperature, low salinity, or high variability in abiotic factors, e.g. driftwood. In our research unit we use E. subulatus and in particular, the comparison with the less stress-tolerant species Ectocarpus siliculosus to study processes of adaptation and acclimation, interactions with bacteria, and sex chromosome evolution and speciation (1,2). However, currently only a very fragmented assembly of the E. subulatus genome is available, limiting these analyses (3).
Project aim: The aim of this project will be to generate a new, high-quality assembly and annotation of the E. subulatus combing Illumina sequencing data with 6Gb newly generated long-read sequences (Oxford Nanopore sequencing, already accomplished) and a HiC data (to be generated parallel to this project). Specifically, the internship will cover the test of alternative base callers for the Nanopore data, the generation of a draft assembly with different assemblers, cleaning (removal of prokaryotic contaminants) and comparison of assemblies, structural annotation (repeated elements, genes, etc.), and functional annotations (predicted gene functions, possibly including the generation of a metabolic network). This will form the bases for updated structural and functional comparisons of E. subulatus and the E. siliculosus, which will also be initiated during the internship.
Profile: For this internship, we are looking for a student motived to discover bioinformatic work in the context of a marine biological laboratory, and with an in interest in adaptation and speciation. The student should be familiar with working in a Unix environment and have a working knowledge of standard bioinformatics tools. Specific training for the required tools and support will be provided on-site. Interactions within the laboratory will be partially in French, partially in English, so basic knowledge of English or the willingness to acquire such knowledge is required.
Duration: Financing is available for a duration of max. 4 months 568,76 Eur per month; the starting date is flexible, but the internship needs to be completed in 2020.
Location: This internship will be carried out with the Laboratory of Integrative Biology of Marine Models at the Roscoff Biological Station. This laboratory consists mainly of biologists working on various marine models (algae, bacteria, sea urchins, sharks), but has tight ties to the local Bioinformatics platform which will provide support during the internship. Roscoff is a small, touristic village on the coast of northern Finistere, Brittany.
1) Dittami SM, Duboscq-Bidot LL, Perennou M, et al. 2016. Host-microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures. ISME Journal 10: 51–63.
2) Lipinska AP, Van Damme EJM, De Clerck O. 2016. Molecular evolution of candidate male reproductive genes in the brown algal model Ectocarpus. BMC Evolutionary Biology 16: 5.
3) Dittami SM, Corre E, Brillet-Gueguen L, et al. 2020. The genome of Ectocarpus subulatus - a highly stress-tolerant brown alga. Marine genomics in press.