Alain Franc - Algae, Protists & Fungi Plenary

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