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PhD Thesis proposal form
Discipline: Biology
Doctoral School
ED 145: Plant Sciences / Sciences du Végétal
http://www.ed-sciences-du-vegetal.u-psud.fr/en/ecoledoctorale.htm
Thesis subject title:
The Genomics of domestication of cheese fungi (Penicillium)
 Laboratory name and web site
Laboratoire Ecologie, Systématique et Evolution
http://www.ese.u-psud.fr/article211.html?lang=en
http://www.ese.u-psud.fr/
 PhD supervisor (contact person):
 Name: Tatiana Giraud
 Position: Directrice de Recherches, Directrice adjointe du laboratoire
 email: [email protected]
 Phone number: +33 1 69 15 56 69
 Thesis proposal (max 1500 words):
Context
Understanding the genetic and genomic processes behind adaptive phenotypes remains a holy grail in
biology. This is not simply an academic exercise; it is also crucial for predicting how organisms will respond
to global crises such as climate change and increasing food demand. Our knowledge of the genomic basis that
underlies the evolutionary processes of adaptation remains in its infancy1. Current key challenges include
identifying the genes involved in ecologically relevant traits as well as understanding the nature, time course,
and architecture of the genomic changes involved in the origin and processes of population adaptation,
divergence, and ecological speciation. These processes will be subsumed below under the term “adaptive
divergence”.
Reaching a new level of understanding of the genomic processes of adaptive divergence requires the
following questions to be addressed: How many genes are involved in adaptive divergence? What traits are
involved? Are particular classes of genes or mutations involved —such as amino-acid substitution, gene
duplications, gene gains, gene losses, or horizontal gene transfers (HGT)? What proportion of the genome is
involved in adaptation? Do independent adaptations to the same environment involve the same genes and
mutations? Do structural genomic rearrangements allow adaptive divergence to take place? Does adaptation
incur costs, such as the fixation of linked deleterious mutations? Is genome evolution mostly driven by
adaptation or by neutral processes? There is surprisingly little data to evaluate these issues, in contrast to the
corpus of theoretical developments2. This is despite their huge importance for human industry, well-being,
food production and health.
Next Generation Sequencing (NGS) technologies can sequence dozens of related genomes, thereby
opening the possibility of approaching these crucial issues from a new perspective. This enables
unprecedented insights into the genomic bases and processes of adaptation3, 4. Candidate genes are identified
as those showing the signature of recent positive selection or divergent adaptation between populations. This
allows ecologically important functions to be identified as well as the understanding of underlying genetic
architecture and genomic processes of adaptation. Sequencing multiple genomes can address the relative
importance of amino-acid substitutions, genomic rearrangements, gene gain, gene loss, and introgressions—
for which relevant data is badly missing so far.
This project will use high-throughput sequencing to investigate processes of adaptive divergence in the
domesticated filamentous fungal species and their wild relatives in the genus Penicillium, which are used for
cheese and antibiotic production. Domestication has been one of the most important innovations throughout
human history and has been used since Darwin as a model for studying evolution. The potential offered by
NGS to sequence multiple genomes of domesticated fungi provides the opportunity to study the response to
human-induced selection from a completely different perspective. Cheese is a substrate with a high content of
protein and fat and has a unique heterogeneous physicochemical composition which supports a complex
ecosystem where many bacteria and fungi compete. To adapt to this particular environment, cheese
filamentous fungi have acquired certain fermentative and competitive activities. The uniformity and
consistency of selective environments may have also relaxed selection on traits other than those involved in
cheese quality. P. camemberti is inoculated during the cheese-making process for soft cheeses, whereas P.
roqueforti is used for blue-veined cheeses. These fungi have been subjected to different domestication
processes. Both domesticated and wild strains exist in the P. roqueforti species, which exhibit high genetic
variability5 and most likely sexual reproduction6. Closely related species occur as food spoilers, such as P.
carneum and P. paneum. In contrast, P. camemberti has never been isolated from other substrates besides
dairy products. The species is the product of various selection programs for improving phenotypes such as the
texture and color of the mycelium or physiological characteristics. P. camemberti is a single clonal lineage
with little genetic variability5. Closely related species occur as food spoilers (P. biforme, P. fuscoglaucum) or
in natural habitats (P. cavernicola). Whole genome sequences of several strains of P. camemberti, P.
roqueforti, P. chrysogenum, P. biforme, P. fuscoglaucum, P. cavernicola, P. carneum and P. paneum are
available.
Objective 1 – Positive selection
Positive selection is one of the most enlightening responses by organisms to domestic selection. Genes
involved in adaptive divergence will be identified through screening genome-wide patterns of DNA
polymorphism for locus-specific signatures of positive directional selection7. Methods for detecting selection
based on allele frequency distributions include Tajima’s D, Fay and Wu’s H, the use of FST, θπ , Dxy, the HKA
test, and a number of other statistics4, 8-11.
Objective 2 – Relaxed selection
Relaxed selection can be identified by the presence of nonsense substitutions, accumulation of transposable
elements, an equal frequency of amino-acid vs. synonymous substitutions, chromosomal rearrangements,
genome shuffling, and modified codon usage12. The genome of P. camemberti seems to have in fact undergone
intensive shuffling.
Objective 3 – Gene gain and gene loss
The existence of niche-specific gene sets13, gene gains14, gene family expansion and loss of superfluous genes
15
has been involved in the domestication of Lactobacillus bacteria to dairy products14 and in symbioses16, 17.
Gene gain or loss will be investigated in the Penicillium strains/species from the cheese environment vs.
closely related strains from other environments.
Objective 4– Islands of low divergence: HGT and introgressions
HGT and introgressions can be a means for organisms to acquire new adaptive traits18, and this will be
investigated among the Penicillium genomes.
Expected impact
The proposed research should yield unprecedented insights into the genomics of adaptive divergence in
eukaryotes. These include the kinds of traits, the genetic architecture of these traits, as well as the genomic regions
and processes involved. We will advance our understanding of the relative importance of amino-acid substitutions,
genomic rearrangements, gene gain, gene loss, introgressions and drift, as well as the proportion of the genome
involved in adaptation. The results will also have direct applied implications for industries that use domesticated
organisms. These questions are not easily addressed in other eukaryotes given their large genomes and the present
project will therefore provide a benchmark to understand adaptation in eukaryotes.
References
1.Bernatchez (2010) Phil Trans R Soc B 365, 1783-1800
2.McKay (2008) Evolution 62, 2953-2957
3.Luikart (2003) Nature Reviews Genetics 4, 981-994
4.Ellison (2011) PNAS 108, 2831-2836
5.Giraud (2010) Int. J. Food Microb. 137 204-213
6.Houbraken (2010) IMA Fungus 1, 171-180
7.Storz (2005) Mol Ecol 14, 671
8.Tajima (1989) Genetics 123, 585-596
9.Nielsen (2009) Genome Res 19, 838-849
10.Fay (2000) Genetics 155, 1405-1413
11.Hudson (1990 ) Science 250 575-575
12.Whittle (2011) Euk Cell 10, 594-603
13.O'Sullivan (2009) BMC Microbiology 9, 50
14.Makarova (2006) PNAS 103, 15611-15616
15.van de Guchte (2006) PNAS 103, 9274-9279
16.van Ham (2003) PNAS 100, 581-586
17.McDowell (2011) PNAS 108, 8921-8922
18.Friesen (2006) Nature Genet. 38, 953-956
 Publications of the laboratory in the field (max 5):
Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, and Giraud T. (2010) Glacial refugia in
pathogens: European genetic structure of anther smut pathogens on Silene latifolia and S.
dioica. PloS Pathogens 6: e1001229.
Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A and Giraud T (2011)
Maintenance of fungal pathogen species that are specialized to different hosts: allopatric
divergence and introgression through secondary contact. Mol Biol Evol 28:459–471.
Yockteng R. Marthey, S. Chiapello, H., Hood, ME, Rodolphe F., Gendrault-Jacquemard A, Devier,
B., Wincker, P., Dossat, C. and Giraud, T. (2007) Expressed sequences tags of the anther
smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes. BMC
Genomics. 8:272.
Aguileta G, Hood ME, Refrégier G, Giraud T (2009) Invited review: Genome evolution in
pathogenic and symbiotic fungi. Advances in Botanical Research. 49: 151-193.
Giraud T, Gladieux P, Gavrilets S. (2010) Linking emergence of fungal plant diseases and ecological
speciation. Trends Ecol Evol 25: 387–395.
 Specific requirements to apply, if any:
Bioinformatics skills would be appreciated; the most important being strong interest in
evolutionary biology