Open PhD position at Roscoff (France)
http://www.sb-roscoff.fr/en
The paradox of being a specialist for a parasite of marine blooming
dinoflagellates
Figure 1: Three examples of eukaryotic parasites infecting the toxic dinoflagellates Alexandrium minutum.
A. Dinomyces sp. (Fungi, chytrid), is a generalist ectoparasite. B. Parvilucifera infectans (Alveolata,
Perkinsozoa) is a generalist endoparasite. C. Amoebophrya sp. (Alveolata, Syndiniales) is a rather specialist
endoparasite.
The parasitism is a frequent lifestyle in nature and a major source of evolutionary pressure
for both the host and the parasite. Given the ubiquity of host-parasite interactions, understanding the
factors that generate, maintain, and constrain these associations is of primary interest with implications
for a wide range of ecological issues, including dynamics of emerging infectious diseases and
invasions (Daszak et al. 2000, Keane and Crawley 2002). Although little studied, many extremely
virulent microeukaryotic parasites infecting microalgae have been detected in the marine plankton.
Among them are Syndiniales, which constitute a diverse and highly widespread group (Guillou et al.
2008). Because of their virulence and abundant offspring, such parasites have the potential to control
dinoflagellate populations, and therefore toxic microalgal blooms (Alves de Souza et al. 2015). These
parasites usually exhibit a narrow host spectrum (Chambouvet et al. 2008). Such specialization
strongly relies on the life-history traits and ecology of the host. However, coastal planktonic
ecosystems are by nature characterized by strong environmental fluctuations and rapid turnovers, even
at the population level (Dia et al. 2014). Considering the short generation time and the high dispersal
capacity of microalgae, their parasites must adapt at a significantly faster rate than for larger hosts (e.g.
plants or animals). All of these considerations should theoretically lead to the natural selection of
generalist parasites at the expense of specialists. The persistence and ecological success of
specialists among marine planktonic parasites is thus an intriguing paradox.
We hypothesise that host specialization is constrained by evolutionary processes underlying
key steps during the infection (such as penetration inside the host and the takeover of the host). We
will explore this hypothesis at the cellular level, using molecular approaches
Strategy
We will screened intra and inter variability of > 70 parasitic strains corresponding to 7 genetic clusters
(based on their ITS). All of these parasites belong to the same genus (Amoebophrya, Syndiniales) and
infect dinoflagellates, but have different host range. NGS reads (RAD and/or MIG-seq) will be
mapped on two complete genomes recently acquired from two strains having contrasting host range
(one specialist and one able to infect several species and at least two genera), and for which a model of
gene prediction is available (using transcripts acquired every 6 hours during a complete life cycle).
Genes under positive selection will be screened with the hypothesis that such genes could be involved
in speciation, host-parasite interactions, or sex determination. Special attention will be given to
homologues with a known function find in other dinoflagellates and closely related parasites such as
Apicomplexa (e.g. Plasmodium falciparum) and Perkinsozoa. Novel hypotheses will be then tested in
the laboratory using living strains. The PhD student will also actively participate in the expert
annotation of genomes, being fully integrated to the international consortium.
Skills
- Strong background in Microbiology
- Knowledge of NGS analysis tools and methods
- Knowledge in population genetics and/or molecular biology
- Ability to work and integrate a team
- Autonomy, rigor and openness
An interview will be done in Paris during June. Applicant, if successful, will start the 1rst of October 2016. The duration of a PhD in France is 3 years. Applications should be sent to Laure Guillou (lguillou@sb-­‐roscoff.fr) before middle of April 2016. Context of the project:
This project is part of the ANR HAPAR (Head L. Guillou), in collaboration with the ABiMS platform
(Analysis and Bioinformatics for Marine Science) at the Station Biologique of Roscoff (France), the
University of Ghent (Belgium, S. Rombauts, Y. Van de Peer), and the Genoscope (France, P.
Wincker, B. Porcel, France).
The student will work at the Station Biologique of Roscoff (UMR7144, France) under the supervision
of L. Guillou (Team Diversity and Interactions in oceanic plankton, http://www.sbroscoff.fr/en/diversity-and-interactions-oceanic-plankton), and will work in a very dynamic group
working on marine plankton (> 50 persons). The Station Biologique of Roscoff has a long tradition in
the study of plankton. Its major achievements include the development of flow cytometry methods
applied to Oceanography, the creation and development of the Roscoff Culture Collection hosting now
more 2500 strains of microalgae, viruses and parasites, and a pioneering role in meta-“omics”
approaches of marine picoeukaryotes from marine environments (TARA cruise, OSD).
Other partners of the project:
The ABiMS bioinformatics platform is dedicated to marine life science (picoplankton, marine
cyanobacteria, etc.). ABiMS team assist researchers with bioinformatic analyses and complex
programming tasks in different ways (workflow, annotation pipeline, databases, etc.), provides a
computational distributed infrastructure support through hardware and resources (tools, data, etc.).
ABiMS develop also information system based on integrated databases and can provide gateway
between -omics and environmental data, to improve interoperability.
The Genoscope, the French National Sequencing Center, now part of the Genomics Institute at the
CEA (Commisariat à l’Énergie Atomique). The Genoscope has more than 15 years working on widely
different eukaryote genomes, from single-cell to complex plants and animals, a rather unique
positioning in French biology. The Genoscope has also developed the skills to critically assess genes
structure and validity through our annotation activity. Different ongoing projects consist in the
analysis of eukaryotic genomes sequenced and annotated at Genoscope (as examples, banana, coffee,
rainbow trout, rapeseed, etc). Recently, Genoscope has been involved in the sequencing and
annotation of algal genomes (Chondrus crispus, a typical red seaweed, Ectocarpus siliculosus, a
brown alga and Bathycoccus prasinos, a widely distributed green alga) and actively participated to the
TARA cruise.
The BioInformatics & Evolutionary Genomics Group at the VIB Department of Plant Systems
Biology in Ghent (http://bioinformatics.psb.ugent.be). This large group has built up a world-wide
recognition in Bioinformatics attested by its publication record, being focusing in three main areas:
Genome annotation & modeling, Systems Biology, Gene & genome evolution. Besides targeting
objectives of its own, the BEG group has a long tradition of collaboration in large genomics consortia
and/or with individual wet lab partners at the bench or in the field, to allow the build-up of knowledge
and know-how from genome data and metadata collected within each specific project. Worth
mentioning, this group has been exploring a large diversity of taxa, from plants, protists, to fungi and
animals, and has thus experience to anticipate and deal with genome novelties, whatever it could be.
Several genomics projects have been focusing on marine species (Mamelliales, diatoms, Ectocarpus,
Zostera ..) quite often in collaboration with French partners from Banyuls, Roscoff and Paris. Some
other projects focused on symbionts, pathogens, pests or parasitoids, in which relationship with the
host was an important aspect of the analysis done in the group.
References:
• Chambouvet A., Morin P., Marie D., Guillou L. (2008). Control of toxic marine dinoflagellate blooms by serial
parasitic killers. Science. 322: 1254-1257.
• Daszak P., Cunningham A. A., Hyatt A. D. (2000). Emerging infectious diseases of wildlife- Threats to
biodiversity and human health. Science. 287:443-449.
• Dia A., Guillou L., Mauger S., Bigeard E., Marie D., Valéro M., Destombe C. (2014). Spatiotemporal changes
in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum.
Molecular Ecology, Molecular Ecology. 23:549-560.
• Guillou, L., Viprey, M., Chambouvet, A., Welsh R. M., Massana, R., Scanlan D.J., Worden A. Z. (2008).
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).
Environmental Microbiology. 10(12): 3349-3365.
• Guillou L. et al. (2013). The protist Ribosomal reference database (PR2): a catalog of unicellular eukaryote
small subunit rRNA sequences with curated taxonomy. Nucleic Acids Research, database issue, 41:D597D604.
• Keane R. M. and Crawley M. J. (2002). Exotic plant invasions and the enemy release hypothesis. TRENDS in
Ecology & Evolution. 17:164-170
• Lepelletier Frédéric, Sergey A. Karpov, Sophie Le Panse, Estelle Bigeard, Alf Skovgaard, Christian Jeanthon,
Laure Guillou. Parvilucifera rostrata sp. nov. (Perkinsozoa), a novel parasitoid that infects planktonic
dinoflagellates (2014a). Protist. 165:31-49
• Lepelletier Frédéric, Sergey A. Karpov, Elisabeth Alacid, Sophie Le Panse, Estelle Bigeard, Esther Garcés,
Christian Jeanthon, Laure Guillou (2014b). Dinomyces arenysensis gen. et sp. nov. (Rhizophydiales,
Dinomycetaceae fam. nov.), a chytrid infecting marine dinoflagellates. Protist. 165:230-244.
• Montagnes D. J. S., Chambouvet A., Guillou L., Fenton A. (2008). Can microzooplankton and parasite
pressure be responsible for the demise of toxic dinoflagellate blooms? Aquatic Microbial Ecology.
53:201-210.