DC8 - Functional and evolutionary genomics of brown algal immune-related genes for the future breeding of pathogen resistance in brown algae

Advisors: Marck Cock, Yacine Badis, Claire Gachon

Location: The research will be performed at the Station Biologique de Roscoff, CNRS and the student will graduate with a PhD of Sorbonne Université.  The Roscoff Biological Station offers access to first class marine experimental facilities as well as genome editing, mass spectrometry, sequencing and bioinformatics platforms.

How to apply for this position
The submission deadline for this project was May 15th, 2024 and we are currently not accepting any new application.

Scientific context:
While the immune systems of animals and land plants have been extensively studied, there is comparatively very little molecular knowledge about the immune system of brown algae, i.e. how do brown algae detect and defend themselves against aggressors?  
The brown alga Ectocarpus sp7 appears as an ideal model to address this question because is infected by two species of intracellular oomycete pathogens, Eurychasma dicksonii [1,2] and Anisolpidium ectocarpii [3,4]. Pathosystems have been maintained for over a decade using Ectocarpus and other brown algae as routine hosts. Laboratory cultures, transcriptomes of infected Ectocarpus, and additional preliminary data are available in the host laboratory to study the interaction with experimental and bioinformatic strategies. Additionally, Ectocarpus sp7. was the first brown alga to have its full genome sequenced [5], which allowed the in-silico identification of putative pathogen receptor families displaying intriguing evolutionary features such as exon shuffling of their LRR or TPR ligand binding domains [6]. Importantly, CRISPR mutagenesis has been recently established on Ectocarpus sp7 [7], making it ideal to inactivate and conduct functional analysis of gene functions in Phaeophycea, especially in the context of host-pathogen interactions. The ongoing Phaeoexplorer project (ttps://phaeoexplorer.sb-roscoff.fr/home/) offers access to the genomes of over 43 brown algal species.

Image

Objectives and candidate profile: 
1) Investigate the contribution of selected defence genes and putative receptors involved in the response of Ectocarpus to oomycete pathogens, using novel CRISPR-KO methodologies coupled to laboratory infections, ddPCR quantification and RNAseq. This axis includes a collaboration and secondment with IAGE, one of PHABB’s non-academic partners, which specialises in the design and delivery of molecular diagnostic solutions. 
2) Annotate LRR-ROCO and NB-ARC-TPR genes, their conservation and structural features across the brown algal tree of life using Phaeoexplorer Data, specifically assessing the conservation of exon shuffling in LRR and TPR domains.  
3) Using emerging Nanopore targeted sequencing strategies and high-end bioinformatic scripts, test for the existence of rapid evolutionary mechanisms (e.g. exon shuffling, somatic recombination), by comparing the structural variation of pathogen receptors in Ectocarpus strains independently cultured for 5 to 20 years.

Thus, this ambitious PhD program revolves around 3 axes involving (1) functional biology, (2) comparative bioinformatics, and (3) long-read sequencing. The ideal candidate should have solid molecular biology skills, and good background in the topics of phytopathology or plant-microbe interactions. A general interest in data analysis and bioinformatics will also be appreciated, although training can be made available for the candidate during the PhD.

Expected Results: 
1) Provide the first demonstration and quantification of the role of major brown algal stress genes in  resistance to pathogens to inform future molecular breeding programs. 
2) Improved knowledge on the diversity and evolution of candidate pathogen-receptors across  43 brown species. 
3) Novel insights in the mechanisms underlying the evolution and diversification of brown algal gene families that are relevant for breeding purposes, i.e. pathogen receptors.

Planned secondment(s): 
At IAGE with Franz Durandet to gain industrial experience and design algal pathogen ddPCR detection probes, 
At UIBK with Sigrid Neuhauser to explore spatiotemporal regulation of selected algal mRNAs, including LRR-ROCO genes at the cellular scale using single molecule FISH.

Supervision: 

Within the UMR 8227, the PhD candidate will be trained and co-supervised Dr Mark Cock and Dr Yacine Badis, both members of the “Algal Genetics” group.
Dr Mark Cock led a research group at the Ecole Normale Superieure de Lyon, and is now head of the Algal Genetics group at SBR. He has over 20 years of experience working on macroalgal developmental biology and established the model Ectocarpus to pioneer brown algal genetics and genomics with the Ectocarpus Genome Project (74 scientists, 4 M€). Mark currently coordinates the large-scale France Génomique project Phaeoexplorer, in which high quality genome sequences for 43 brown algal species have been obtained, that are currently annotated by a consortium of 110 scientists worldwide.
Dr Yacine Badis specialises on algal-oomycete interactions and holds an associate professor position since 2021 at SBR, where he developed the first effective CRISPR gene knock-out strategy in brown algae. A trained oomycete molecular phytopathologist, Yacine acquired extensive experience of macroalgal pathogen isolation and culturing during three years under the direction of Pr. Claire Gachon. He (co)-authored over 23 peer-reviewed publications, currently leads a WP in the french ANR project HaloGene, and has been recently awarded an ANR JCJC (2024-2027) and Sorbonne Emergence (2024-2025) project to study brown algae and their interactions with marine oomycete effectors.

References: 
[1]  D. G. Müller, F. C. Küpper, and H. Küpper, “Infection experiments reveal broad host ranges of Eurychasma dicksonii (Oomycota) and Chytridium polysiphoniae (Chytridiomycota), two eukaryotic parasites in marine brown algae (Phaeophyceae),” Phycol. Res., vol. 47, no. 3, pp. 217–223, Sep. 1999.

[2]  C. M. M. Gachon, M. Strittmatter, D. G. Müller, J. Kleinteich, and F. C. Küpper, “Detection of Differential Host Susceptibility to the Marine Oomycete Pathogen Eurychasma dicksonii by Real-Time PCR: Not All Algae Are Equal,” Appl Env. Microbiol, vol. 75, no. 2, pp. 322–328, 2009.

[3] C. M. M. Gachon, M. Strittmatter, Y. Badis, K. I. Fletcher, P. Van West, and D. G. Müller, “Pathogens of brown algae: culture studies of Anisolpidium ectocarpii and A. rosenvingei reveal that the Anisolpidiales are uniflagellated oomycetes,” Eur. J. Phycol., vol. 52, no. 2, pp. 133–148, 2017.  

[4] P. Murúa, D. G. Müller, M. Etemadi, P. West, and C. M. M. Gachon, “Host and pathogen autophagy are central to the inducible local defences and systemic response of the giant kelp Macrocystis pyrifera against the oomycete pathogen Anisolpidium ectocarpii,” New Phytol., vol. 226, no. 5, pp. 1445–1460, Jun. 2020.

[5] J. M. Cock et al., “The Ectocarpus genome and the independent evolution of multicellularity in brown algae,” Nature, vol. 465, no. 7298, pp. 617–621, 2010.

[6] Zambounis A, Elias M, Sterck L, Maumus F, Gachon CM. "Highly dynamic exon shuffling in candidate pathogen receptors ... what if brown algae were capable of adaptive immunity?" Mol Biol Evol. 2012 Apr;29(4):1263-76. 

[7] Y. Badis et al., “Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus,” New Phytol., vol. 231, no. 5, pp. 2077–2091, Sep. 2021.