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PhD position in Population
Genomics of Fungi
I am looking for a highly motivated candidate to
work on a population genetics/genomics project in the
plant pathogenic species Melampsora larici-populina
(responsible for the poplar rust). The aim of the PhD is to highlight
the virulence factors of this fungal plant pathogen from a population
genomic approach. Candidates should have a good background in
evolutionary ecology and above all population genetics. Knowledge on
host parasite interactions would be appreciated. Interest (but not
necessarily good skills) in molecular biology (next generation
sequencing) is required.
The proposed project stands at the core of the joint unit
Tree-Microorganism interactions (located near Nancy, East part of
France) and lies at the interface of its two major teams “ecology and
population biology of tree fungal pathogens (directed by B. Marçais)
and “eco-genomics” (directed by F. Martin). The junior scientist will
thus benefit from the complementary skills and resources of these two
teams, including advanced population genetics knowledge, large and
historical population sampling on one hand and, on the other hand,
great genomics tool and molecular resources, including genome sequence
and transcriptomic analyses performed on this model pathogen species.
The subject has been selected for application as
“Young scientist contracts” which result from a
partnership between INRA and graduate schools. These contracts have
initial duration of 3 years (PhD) and can be renewed for 2 more years
for a post doc project (including necessarily a period of time abroad).
Young scientist contracts have very attractive remuneration conditions.
Before obtaining his/her PhD, the doctoral student receives 2055€
(gross) per month. After obtaining his/her PhD, the remuneration is 2373€
(gross) per month. An annual bonus of 796€ is paid
half-yearly. More details on
young scientist contracts can be found at
Successful candidate will be selected by an examination
committee of the graduate school RP2E (
http://www.rp2e.inpl-nancy.fr/index.php?id=5
The competitive examination is open to any nationality.
Dead line for application is May 15th. Position will start
in fall 2010.
Don’t hesitate to contact me for any query
(halkett@nancy.inra.fr).
Below is the abstract of the subject I propose.
The field of population genomics has recently
emerged at the cross between traditional population genetics and the
development of high-throughput techniques, with the aim to decipher the
strength of selection events on genome evolutions. Although not yet
widely applied to plant pathology studies, these approaches seem
particularly well suited to reveal the genetic bases of the adaptive
potential of fungal plant pathogens. While the rapid pace of pathogen
evolution (which result from intensive selection pressure through the
massive deployment of resistant genes) presents a major impediment to
sustainable agriculture, it also provides interesting opportunities to
better understand the evolutionary biology of host–parasite
interactions. Here we want to apply the population genomic toolboxes to
decipher the evolution of virulence loci in the fungus responsible for
the poplar rust (Melampsora larici-populina). Deepening
into the genome’s organisation, the project will successively try to
(i) highlight genomic regions subjected to a selective sweep caused by
a drastic selection event which was the overcoming of a major resistant
gene, (ii) point out the genes (among these region) under positive
selection, and putatively responsible for the gene for gene interaction
and (iii) study the evolution, including recombination rate, of these
genomic regions implied in fungal pathogenicity. This project would
thus bring us fundamental knowledge on the genome evolution of
pathogens, which would help designing sustainable strategies of crop
protection.