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

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

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  1. R-SYST Fungi : a French consortium for fungalbarcoding and taxonomic identification V. Laval, M. Buée , MH Lebrun , R-SYST Fungi consortium and Alain Franc

  2. Few individuals Many traits : genomewidecover Manyindividuals Few DNA regions of interest

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

  4. 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

  5. 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

  6. 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

  7. 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/

  8. 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)

  9. 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

  10. 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)

  11. 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

  12. 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

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

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

  15. Russulamaculata Thelephoracaryophyllea Inocybe griseolilacina

  16. 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

  17. 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

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