1. V. Laval, M. Buée , MH Lebrun , R-SYST Fungi
consortium and Alain Franc

3. Few Many traits :
individuals genome wide cover
Many individuals
Few DNA regions of interest

4. Where and who are we ?
How many ?
About 60

5. A common network: Stakes
1 – to feed a common database
2 – to have common methodological exchanges
3 – Develop bioinformatics tools for taxonomy and biodiversity
4 – For diagnostics and inventories
5 – Develop metagenomics for taxonomy
6 – Access to High Performance Computing
7 – getting involved in international networks

6. Scheme of French fungal research laboratories
BIO3P Resistance, Adaptation of Populations and Durability
Phytophthora infestans; Mycosphaerella pinodes, Phoma Lille university
medicaginis var pinodella, Aphanomyces euteiches, Leptosphaeria Laboratory of botanic
maculans, L. biglobosa, Gaeumannomyces graminis var. tritici and mycology
- Evolutionary Ecology of Fungal Pathosystems Venturia/malus trees
- fungal necrotrophe complexes :(Alternaria)
IaM
-biology and genetic of macroscopic fungi (agaricus)
ESV
-study on mycotoxines (fusarium) BIO3P LIPP
pathogens in trees (alien fungi, Sphaerospis sapinea
and Fusarium circinatum, oak powdery mildew )
(Fungi associated to grapevine)
sustainable interaction beetween mycorrhizal symbionts,
: (glomeromycota)
Soil and environment microbiology
(Soil fungal community, soil fingal pathogenes)
Cereal disease (fusarium)
Interactions
Crop legume Sclerotinia sclerotiorum, Oidium neolycopersici,
Tree Ceratocystis fimbriata f. sp. platani,
CIRM Biotiques et
Santé Végétale
fungi and tropical trees Colletotrichum kahawae; Fusarium xylarioides;
Mycosphaerella fijiensis
species distribution of ectomycorrhizal fungi in the environment and
genetic diversity within populations of these fungi.
Interactions
Biotiques et oomycetes
Santé Végétale

7. R-syst fungi network coordinated by two groups from INRA
1)
Bioger_CPP biology and management of agricultural hazard _ plant
pathogens fungi unit
Bioger develops research on fungal plant pathogens, including their genome
analysis (Leptosphaeria, Botrytis, Blumeria) and their evolution, in particular
during their adaptation to control methods (plant resistance, fungicides)
A multidisciplinary project to study pathogenic fungi from gene to field :
- Genomics - Biology/Molecular Genetics - Biochemistry
- Population Genetics and Evlution
- Epidemiology and population dynamics
- Control of fungal diseases
Unit leader : MH Lebrun
Fungal R-syst and diagnostic: V Laval

8. 2) Ecogenomics of Interactions Lab (tree-
microbes interactions Unit)
This group conducts research on the biology and ecology of
tree-associated fungi (mycorrhizal fungi, pathogens and
saprobes) in forest ecosystems.
The « tree-microbes interactions » is structured according
to three main themes:
(1) Structural et functional genomic of trees and associates
fungi
(2) Molecular physiology of biotrophic interactions
(3) Ecology of forest fungi, with a particular interest in the
community ecology of mycorrhizal fungi and on the
causes of emergence of pathogenic fungi.
Lab leader: F. Martin & Pascale Frey-Klett
Fungal R-syst and Ecology topic: M. Buée
http://mycor.nancy.inra.fr/

9. These two units combine knowledge on several genera
On pathogen from crops
Leptosphaeria, Botrytis, Blumeria, Mycosphaerella, Fusarium,
Microdochium, Puccinia
On ectomycorrhizal fungi
Hebeloma,, Laccaria, Lactarius, Piloderma, Pisolithus, Oidiodendron, Tuber and
Glomus Genome Ressources
On saprobes and forest pathogens
Heterobasidion, Serpula, Melampsora Genome Ressources
Fungal species collection (cultures of fungal strains
and herbarium)

10. More…
An internationnal biological ressource
center (CIRM)
Filamentous fungi involved in the transformation of plant biomass, mainly
basidiomycetes and to a lesser extent ascomycetes.
Laboratory of Mycology ( )
This lab promotes reference methods of analysis in mycology and to participate in
the elaboration of national/international standards to the biological control and
sustainable pathogen management.
French fungal community skilled and dispersed

11. But also some fungal systematicians
- taxinomy,
- systematic,
- ecology,
- toxicology
Museum (MNHN) : 500 000 specimens and a collection of 4 000 fungal
strains
Biology et taxonomy of microfungi group (Joëlle Dupont, MNHN)

12. French Mycological Societies and academic research
One French mycological society, but numerous local mycological societies of
regional federations (e.g. Fédération Mycologique de l’Est, FME)
Few collaborations between actors of these societies and the academic research
domain
Coll. Between INRA Nancy and JP Maurice ( AMYPHAR Society)
About ten common publications

13. What has been built …
1 – Buy seven servers: Angers, Grignon, Orléans, Nancy
Thonon, Montpellier, Bordeaux
2 – Common database written and implemented
3 – Feeding in connection with NCBI and BOLD in due course
4 – Building bioinformatics toolboxes, in connection with CBoL Portal

14. James et al. ; Nature 2006, Vol 443, 818-822

15. Two useful notions on graphs
Homology within
Clique
Connex component theshold
Basis for Phylogenetics
Basis for BLAST
Ultrametrics
Finding: easy
Finding: hard (NP complete)

16. Puechabon, all -- gap = 30
Russula maculata
40
Thelephora caryophyllea
Size of connex components
30
Inocybe griseolilacina
20
10
0
0 50 100 150 200 250
Rank of connex component

17. Fungal diversity and community structure along altitudinal
gradients in Europe: metagenomic approach
VOSGES Pyrosequencing
ALPS Quality filter
PYRENEES
GUADARRAMA APENNINES Clustering (Uclust)
MOTU (97%)
BLASTN (NCBI)
Pinus sylvestris (9 altitudes)
Fagus sylvatica (11 altitudes) 240 < Nb of OTUs < 350
UE Baccara project 17

18. Factors influence fungal species assemblage Results
Fagus sylvatica
Alpes (3)
1.5
Pyrénées
Pyrenees (5)
Vosges (3)
1.0
0.5
AFC Axe 1
12.2%
0.0
1.0
-0.5
0.5
-1.0
0.0
23.6%
AFC Axe 2
-0.5
4.0 4.5 5.0 5.5 6.0
Soil pH
-0.5 0.0 0.5 1.0
-1.5
AFC Axe 2
-2.5
-1.0 -0.5 0.0 0.5 1.0 1.5
AFC Axe 1
-1.5
Soil pH = 1st factor
-2.5
Temperature = 2nd factor 6 8 10 12
Mean annual temperature (°C) 18