Open PhD position at Roscoff (France)

The paradox of being a specialist for a parasite of marine blooming

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


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.


– 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

Applications should be sent to Laure Guillou (

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,…/diversity-and-interactions-ocean…
),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

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 (
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


– 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., Valero 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,

– Keane R. M. and Crawley M. J. (2002). Exotic plant invasions and the
enemy release hypothesis. TRENDS in Ecology & Evolution. 17:164-170

– Lepelletier Frederic, 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 Frederic, Sergey A. Karpov, Elisabeth Alacid, Sophie
Le Panse, Estelle Bigeard, Esther Garces, 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.
Le 07/07/2016 Ã 18:26, Brian Golding a ecrit :

Laure Guillou, Directrice de recherche CNRS
Station Biologique de Roscoff
Place Georges Teissier, CS 90074
29688 ROSCOFF CEDEX France
Phone: +33 2 98 29 25 63

UMR7144, leader of the team “Diversity and Interactions in the Oceanic Plankton”