Alain Franc - Algae, Protists & Fungi Plenary


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Alain Franc - Algae, Protists & Fungi Plenary

  1. 1. V. Laval, M. Buée , MH Lebrun , R-SYST Fungi consortium and Alain Franc
  2. 2. Few Many traits :individuals genome wide coverMany individuals Few DNA regions of interest
  3. 3. Where and who are we ?How many ? About 60
  4. 4. 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
  5. 5. Scheme of French fungal research laboratoriesBIO3P 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.InteractionsBiotiques et oomycetesSanté Végétale
  6. 6. R-syst fungi network coordinated by two groups from INRA 1)Bioger_CPP biology and management of agricultural hazard _ plantpathogens fungi unitBioger develops research on fungal plant pathogens, including their genomeanalysis (Leptosphaeria, Botrytis, Blumeria) and their evolution, in particularduring 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. 7. 2) Ecogenomics of Interactions Lab (tree- microbes interactions Unit)This group conducts research on the biology and ecology oftree-associated fungi (mycorrhizal fungi, pathogens andsaprobes) in forest ecosystems.The « tree-microbes interactions » is structured accordingto 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
  8. 8. These two units combine knowledge on several generaOn pathogen from cropsLeptosphaeria, Botrytis, Blumeria, Mycosphaerella, Fusarium,Microdochium, PucciniaOn ectomycorrhizal fungiHebeloma,, Laccaria, Lactarius, Piloderma, Pisolithus, Oidiodendron, Tuber andGlomus Genome RessourcesOn saprobes and forest pathogensHeterobasidion, Serpula, Melampsora Genome RessourcesFungal species collection (cultures of fungal strainsand herbarium)
  9. 9. More… An internationnal biological ressource center (CIRM)Filamentous fungi involved in the transformation of plant biomass, mainlybasidiomycetes and to a lesser extent ascomycetes.Laboratory of Mycology ( )This lab promotes reference methods of analysis in mycology and to participate inthe elaboration of national/international standards to the biological control andsustainable pathogen management.French fungal community skilled and dispersed
  10. 10. But also some fungal systematicians - taxinomy, - systematic, - ecology, - toxicologyMuseum (MNHN) : 500 000 specimens and a collection of 4 000 fungalstrainsBiology et taxonomy of microfungi group (Joëlle Dupont, MNHN)
  11. 11. French Mycological Societies and academic researchOne French mycological society, but numerous local mycological societies ofregional federations (e.g. Fédération Mycologique de l’Est, FME)Few collaborations between actors of these societies and the academic researchdomainColl. Between INRA Nancy and JP Maurice ( AMYPHAR Society)About ten common publications
  12. 12. 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
  13. 13. James et al. ; Nature 2006, Vol 443, 818-822
  14. 14. Two useful notions on graphs Homology within Clique Connex component theshold Basis for Phylogenetics Basis for BLAST Ultrametrics Finding: easy Finding: hard (NP complete)
  15. 15. Puechabon, all -- gap = 30 Russula maculata 40 Thelephora caryophylleaSize of connex components 30 Inocybe griseolilacina 20 10 0 0 50 100 150 200 250 Rank of connex component
  16. 16. 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 < 350UE Baccara project 17
  17. 17. 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