alain franc - algae, protists & fungi plenary
TRANSCRIPT
R-SYST Fungi : a French consortium for fungal barcoding and taxonomic identification
V. Laval, M. Buée , MH Lebrun , R-SYST Fungi consortium and Alain Franc
Few individuals
Many traits : genome wide cover
Many individuals
Few DNA regions of interest
Where and who are we ?
How many ?
About 60
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
Scheme of French fungal research laboratoriesBIO3P
Resistance, Adaptation of Populations and Durability Phytophthora infestans; Mycosphaerella pinodes, Phoma medicaginis var pinodella, Aphanomyces euteiches, Leptosphaeria maculans, L. biglobosa, Gaeumannomyces graminis var. tritici
- fungal necrotrophe complexes :(Alternaria)
sustainable interaction beetween mycorrhizal symbionts, : (glomeromycota)
- Evolutionary Ecology of Fungal Pathosystems Venturia/malus trees
BIO3P
-biology and genetic of macroscopic fungi (agaricus)-study on mycotoxines (fusarium)
Interactions Biotiques et Santé Végétale
IaM
CIRM
Lille universityLaboratory of botanic and mycology
Cereal disease (fusarium)
(Soil fungal community, soil fingal pathogenes)
(Fungi associated to grapevine)
pathogens in trees (alien fungi, Sphaerospis sapinea and Fusarium circinatum, oak powdery mildew )
Soil and environment microbiology
Crop legume Sclerotinia sclerotiorum, Oidium neolycopersici,Tree Ceratocystis fimbriata f. sp. platani,
Interactions 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.
oomycetes
ESV
LIPP
R-syst fungi network coordinated by two groups from INRA
1)
Bioger_CPP biology and management of agricultural hazard _ plant pathogens fungi unit
Unit leader : MH LebrunFungal R-syst and diagnostic: V Laval
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
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-KlettFungal R-syst and Ecology topic: M. Buée
2)
http://mycor.nancy.inra.fr/
Ecogenomics of Interactions Lab (tree-microbes interactions Unit)
These two units combine knowledge on several genera
Leptosphaeria, Botrytis, Blumeria, Mycosphaerella, Fusarium, Microdochium, Puccinia
On pathogen from crops
On ectomycorrhizal fungi
Hebeloma,, Laccaria, Lactarius, Piloderma, Pisolithus, Oidiodendron, Tuber and Glomus Genome Ressources
On saprobes and forest pathogensHeterobasidion, Serpula, Melampsora Genome Ressources
Fungal species collection (cultures of fungal strainsand herbarium)
French fungal community skilled and dispersed
Filamentous fungi involved in the transformation of plant biomass, mainly basidiomycetes and to a lesser extent ascomycetes.
An internationnal biological ressource center (CIRM)
More…
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.
But also some fungal systematicians
Museum (MNHN) : 500 000 specimens and a collection of 4 000 fungal strainsBiology et taxonomy of microfungi group (Joëlle Dupont, MNHN)
- taxinomy,- systematic, - ecology,- toxicology
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 domainColl. Between INRA Nancy and JP Maurice ( AMYPHAR Society)
About ten common publications
What has been built …
1 – Buy seven servers: Angers, Grignon, Orléans, NancyThonon, 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
James et al. ; Nature 2006, Vol 443, 818-822
Two useful notions on graphs
Clique
Basis for PhylogeneticsUltrametrics
Finding: hard (NP complete)
Connex component
Basis for BLASTFinding: easy
Homology withintheshold
0 50 100 150 200 250
01
02
03
04
0
Rank of connex component
Siz
e o
f co
nn
ex
com
po
ne
nts
Puechabon, all -- gap = 30
Russula maculata
Thelephora caryophyllea
Inocybe griseolilacina
17
GUADARRAMA
VOSGES
PYRENEES
ALPS
APENNINES
Fungal diversity and community structure along altitudinal gradients in Europe: metagenomic approach
Pinus sylvestris (9 altitudes)Fagus sylvatica (11 altitudes)
UE Baccara project240 < Nb of OTUs < 350
Pyrosequencing
Quality filter
Clustering (Uclust)
MOTU (97%)
BLASTN (NCBI)
18
-1.0 -0.5 0.0 0.5 1.0 1.5
-2.5
-1.5
-0.5
0.0
0.5
1.0
AFC Axe 1
AFC
Axe
2 23.6%
12.2%
AlpesPyreneesVosges
Alpes (3)Pyrénées (5)Vosges (3)
Soil pH = 1st factorTemperature = 2nd factor
4.0 4.5 5.0 5.5 6.0
-1.0
-0.5
0.0
0.5
1.0
1.5
Soil pH
AF
C A
xe
1
6 8 10 12
-2.5
-1.5
-0.5
0.0
0.5
1.0
Mean annual temperature (°C)
AF
C A
xe
2
Results
Fagus sylvatica
Factors influence fungal species assemblage