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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.

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r syst fungi a french consortium for fungal barcoding and taxonomic identification

R-SYST Fungi : a French consortium for fungalbarcoding and taxonomic identification

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

slide3

Few individuals

Many traits :

genomewidecover

Manyindividuals

Few DNA regions of interest

where and who are we
Where and who are we ?

How many ?

About 60

a common network stakes
A common network: Stakes

1 – to feed a commondatabase

2 – to have commonmethodological exchanges

3 – Developbioinformaticstools for taxonomy and biodiversity

4 – For diagnostics and inventories

5 – Developmetagenomics for taxonomy

6 – Access to High Performance Computing

7 – gettinginvolved in international networks

slide6

Scheme of French fungalresearchlaboratories

BIO3P

Resistance, Adaptation of Populations and Durability

Phytophthora infestans; Mycosphaerellapinodes, Phomamedicaginis var pinodella, Aphanomyceseuteiches, Leptosphaeriamaculans, L. biglobosa, Gaeumannomycesgraminis var. tritici

Lille university

Laboratory of botanic and mycology

- Evolutionary Ecology of Fungal PathosystemsVenturia/malus trees

- fungalnecrotrophe complexes :(Alternaria)

IaM

ESV

-biology and genetic of macroscopicfungi(agaricus)

-study on mycotoxines (fusarium)

LIPP

BIO3P

pathogens in trees (alien fungi, Sphaerospissapinea and Fusariumcircinatum, oak powdery mildew )

  • (Fungiassociated to grapevine)

sustainable interaction beetweenmycorrhizalsymbionts, : (glomeromycota)

Soil and environment microbiology

(Soilfungalcommunity, soilfingalpathogenes)

Cerealdisease(fusarium)

Interactions Biotiques et Santé Végétale

CroplegumeSclerotiniasclerotiorum, Oidiumneolycopersici,

TreeCeratocystisfimbriataf. sp. platani,

CIRM

fungi and tropical treesColletotrichumkahawae; Fusariumxylarioides;

Mycosphaerellafijiensis

species distribution of ectomycorrhizal fungi in the environment and genetic diversity within populations of these fungi.

Interactions Biotiques et Santé Végétale

oomycetes

slide7

R-systfungi network coordinated by two groups from INRA

1)

Bioger_CPPbiologyand managementof agricultural hazard_ plant pathogensfungi unit

Biogerdevelopsresearchon 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

slide8

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 » isstructuredaccording to three main themes:
  • Structural et functionalgenomic of trees and associatesfungi
  • Molecularphysiology of biotrophic interactions
  • Ecology of forestfungi, with a particularinterest in the communityecology of mycorrhizalfungi and on the causes of emergence of pathogenicfungi.

Lab leader: F. Martin & Pascale Frey-Klett

Fungal R-syst and Ecologytopic: M. Buée

http://mycor.nancy.inra.fr/

slide9

Thesetwounits combine knowledge on severalgenera

On pathogenfromcrops

Leptosphaeria, Botrytis, Blumeria, Mycosphaerella, Fusarium, Microdochium, Puccinia

On ectomycorrhizalfungi

Hebeloma,, Laccaria, Lactarius, Piloderma, Pisolithus, Oidiodendron, Tuber and Glomus Genome Ressources

On saprobes and forestpathogens

Heterobasidion, Serpula, MelampsoraGenome Ressources

Fungalspecies collection (cultures of fungalstrains

and herbarium)

slide10

More…

An internationnalbiological ressource center (CIRM)

Filamentous fungi involved in the transformation of plant biomass, mainly basidiomycetes and to a lesser extent ascomycetes.

Laboratory of Mycology ( )

This labpromotesreferencemethods of analysis in mycology and to participate in the elaboration of national/international standards to the biological control and sustainablepathogen management.

French fungalcommunityskilled and dispersed

slide11

But alsosomefungalsystematicians

  • taxinomy,
  • systematic,
  • ecology,
  • - toxicology

Museum (MNHN) : 500 000 specimens and a collection of 4 000 fungalstrains

Biology et taxonomy of microfungi group (Joëlle Dupont, MNHN)

slide12

French Mycological Societies and academic research

  • One French mycological society, but numerous local mycological societies of regional federations (e.g. FédérationMycologique 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
what has been built
What has been built …

1 – Buyseven servers: Angers, Grignon, Orléans, Nancy

Thonon, Montpellier, Bordeaux

2 – Common databasewritten and implemented

3 – Feeding in connectionwith NCBI and BOLD in due course

4 – Building bioinformaticstoolboxes, in connectionwithCBoL Portal

two useful notions on graphs
Two useful notions on graphs

Homologywithin

theshold

Clique

Basis for Phylogenetics

Ultrametrics

Finding: hard (NP complete)

Connex component

Basis for BLAST

Finding: easy

slide16

Russulamaculata

Thelephoracaryophyllea

Inocybe griseolilacina

slide17

VOSGES

ALPS

PYRENEES

APENNINES

Fungal diversity and community structure along altitudinal gradients in Europe: metagenomic approach

Pyrosequencing

Qualityfilter

Clustering (Uclust)

MOTU (97%)

BLASTN (NCBI)

GUADARRAMA

Pinussylvestris(9 altitudes)

Fagussylvatica(11 altitudes)

240 < Nb of OTUs< 350

UE Baccara project

slide18

12.2%

23.6%

Alpes

Alpes (3)

Pyrenees

Pyrénées (5)

Vosges

Vosges (3)

Factors influence fungal species assemblage

Results

Fagus sylvatica

  • Soil pH = 1st factor
  • Temperature = 2nd factor