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Acta Botanica Gallica
Botany Letters
Volume 151, 2004 - Issue 1
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Original Articles

Une classification mycologique phylogénétique francophone (en 2003)

&
Pages 73-102 | Received 10 Feb 2003, Accepted 02 Nov 2003, Published online: 26 Apr 2013

BIBLIOGRAPHIE

  • Almaraz , T. , Roux , C. , Maumont , T. and Durrieu , G. 2002 . Phylogenetic relationships among smut fungi paraziting Dicotyledons based on ITS sequences analysis. . Mycol. Res. , 106 : 541 – 548 .
  • Baldauf , S. L. 1999 . A search for the origins of animals and fungi: comparing and combining molecular data. . Am. Nat. , 154 : S178 – S188 .
  • Baldauf , S. L. 2003 . The deep roots of eukaryotes. . Science , 300 : 1703 – 1706 .
  • Baldauf , S. L. and Doolittle , W. F. 1997 . Origin and evolution of the slime molds (Mycetozoa). . Proc. Natl. Acad. Sci. U.S.A. , 94 : 12007 – 12012 .
  • Baldauf , S. L. and Palmer , J. D. 1993 . Animal and fungi are each other's closest relatives: congruent evidence from multiple proteins. . Proc. Natl. Acad. Sci. U.S.A. , 90 : 11558 – 11562 .
  • Baldauf , S. L. , Roger , A. J. , Wnek-Siefert , I. and Doolittle , W. F. 2000 . A kingdom-level phylogeny of eukaryotes based on combined protein data. . Science , 290 : 972 – 977 .
  • Bapteste , E. , Brinkmann , H. , Lee , J. A. , Moore , D. V. , Sensen , C. W. , Gordon , P. , Durufle , L. , Gaasterland , T. , Lopez , P. , Muller , M. and Philippe , H. 2002 . The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba . Mastigamoeba. Proc. Natl. Acad. Sci. U.S.A. , 99 : 1414 – 1419 .
  • Bauer , R. , Begerow , D. , Oberwinkler , F. , Piepenbring , M. and Berbee , M. L. 2001 . “ Ustilaginomycetes. In: The Mycota, VII B ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 229 – 245 . Berlin : Springer- Verlag .
  • Binder , M. and Hibbett , D. S. 2002 . Higher level phylogenetic relationships of homobasidiomycetes inferred from four rDNA regions. . Mol. Phyl. Evol. , 22 : 76 – 90 .
  • Boidin , J. , Mugnier , J. and Canales , R. 1998 . Taxonomie moléculaire des Aphyllophorales. . Mycotaxon , 66 : 445 – 491 .
  • Borchiellini , C. , Boury-Esnault , N. , Vacelet , J. and Parco , Y. L. 1998 . Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi. . Mol. Biol. Evol. , 15 : 647 – 655 .
  • Bridge , P. 2002 . The history and application of molecular mycology. . Mycologist , 16 : 90 – 99 .
  • Bruns , T. D. , Fogel , R. , White , T. J. and Palmer , J. D. 1989 . Accelerated evolution of a false truffle from a mushroom ancestor. . Nature , 339 : 140 – 142 .
  • Bruns , T. D. , Szaro , T. M. , Gardes , M. , Cullings , K. W. , Pan , J. J. , Taylor , D. L. , Horton , T. R. , Kretzer , A. , Garbelotto , M. and Li , Y. 1998 . A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis. . Mol. Ecol. , 8 : 257 – 272 .
  • Bulman , S. R. , Kuhn , S. F. , Marshall , J. W. and Schnepf , E. 2001 . A phylogenetic analysis of the SSU rRNA from members of the Plasmodiophorida and Phagomyxida. . Protist , 152 : 43 – 51 .
  • Burki , F. , Berney , C. and Pawlowski , J. 2002 . Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. . Protist , 153 : 251 – 60 .
  • Cavalier-Smith , T. 2001 . “ What are fungi? In: The Mycota VII A ” . In Systematics and Evolution. 3 – 37 . D.J. McLaughlin, E.G. McLaughlin & P.A. Lemke (Eds) Springer- Verlag, Berlin
  • Cavalier-Smith , T. , Allsop , M. T.E.P. and Chao , E. E. 1994 . Thraustochytrids are chromists, not fungi: 18S rRNA signatures of Heterokonta. . Philos. Trans. Roy. Soc. Lond. , 339 : 139 – 146 . ser. B
  • Courtecuisse , R. 2001 . Définition et systématique actuelles du règne fongique. . Bull. Sem. Soc. Mycol. Nord , 69 : 3 – 31 .
  • Courtecuisse , R. and Van Haluwyn , C. 1991 . La classification des champignons. . Bull. Sem. Soc. Mycol. Nord , 49–50 : 3 – 82 .
  • Crantz , H. N. 1766 . Institutiones Rei Herbariae. Kraus Praefatio, Vienne.
  • Darlu , P. and Tassy , P. 1993 . La reconstitution phylogénétique. Masson, Paris 245
  • Demoulin , V. 1985 . The red alga—higher fungi phylogenetic link: the last ten years. . Biosystems , 18 : 347 – 356 .
  • Dick , M. W. 2001a . Straminipilous fungi. Kluwyers Academic Publishers, Dortrecht. XV + 670
  • Dick , M. W. 2001b . “ The Perenosporomycetes. In: The Mycota VII A ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 39 – 72 . Berlin : Springer-Verlag .
  • Dick , M. W. , Vick , M. C. , Gibbinsn , J. G. , Hedderson , T. A. and Lopez Lastra , C. C. 1999 . Mycol. Res. , 103 : 1119 – 1125 . 18S rDNA for species of Leptolegnia and other Peronosporomycetes: justification of the suclass taxa Saprolegniomycetidae and Peronosporomycetidae and division of the Saprolegniaceae sensu lato in Leptolegniaceae and Saprolegniaceae
  • Down , G. 2002 . Fungal families trees—finding relationships from molecular data. . Mycologist , 16 : 51 – 58 .
  • Duncan , J. and Cooke , D. 2002 . Identifying, diagnosing and detecting Phytophthora by molecular methods. . Mycologist , 16 : 59 – 66 .
  • Durrieu , G. 2002 . Faut-il avoir peur de la biologie moléculaire? . Lettre de la SMF , 1 : 4 – 5 .
  • Edman , J. C. , Kovacs , J. A. , Masur , H. , Santi , D. V. , Elwood , H. J. and Sogin , M. L. 1988 . Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. . Nature , 334 : 519 – 522 .
  • Eriksson , O. E. , Barai , H.-O. , Currah , R. S. , Hansen , K. , Kurtzman , C. P. , Rambold , G. and Laessoe , T. 2001 . Outline of Mycota. . Myconet , 7 : 1 – 88 . (http://www.umu.se/myconet/Myconet.html).
  • Fell , J. W. , Boekhout , T. , Fonseca , A. and Sampaio , J. P. 2001 . “ Basidiomycetous yeasts. In: The Mycota VII B ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 3 – 35 . Berlin : Springer-Verlag .
  • Förster , H. , Coffey , M. D. , Elwood , H. and Sogin , M. L. 1990 . Sequence analysis of the small subunit ribosomal RNA of three zoosporic fungi and implications for fungal evolution. . Mycologia , 82 : 306 – 312 .
  • Gargas , A. , Depriest , P. T. , Grube , M. and Tehler , A. 1995 . Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. . Science , 268 : 1492 – 1495 .
  • Geiser , D. M. and LoBuglio , K. F. 2001 . “ The monophyletic Plectomycetes: Ascosphaeriales, Onygenales, Eurotiales. In: The Mycota VII A ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 201 – 219 . Berlin : Springer-Verlag .
  • Gernandt , S. G. , Platt , J. L. , Stone , J. K. , Spatafora , J. W. , Hoist-Jensen , A. , Hamelin , R. C. and Kohn , L. M. 2001 . Phylogenetics of helotiales and Rhytismatales based on partial subunit nuclear ribosomal sequences. . Mycologia , 93 : 915 – 933 .
  • Hausner , G. , Belkhiri , A. and Klassen , G. R. 2000 . Phylogenetic analysis of the small subunit ribosomal RNA gene of the hyphochytrid . Rhizidiomyces apo-physatus. Can. J. Bot. , 78 : 124 – 128 .
  • Hibbett , D. S. and Donoghue , M. J. 1995 . Progress toward a phylogenetic classification of the Polyporaceae through parsimony analyses of mitochondrial ribosomal DNA sequences. . Can. J. Bot. , 73 (S1), S853- S861
  • Hibbett , D. S. , Gilbnert , L. B. and Donoghue , M. J. 2000 . Evolutionnary instability of ectomycorrhizal symbioses in Basidiomycetes. . Nature , 407 : 506 – 508 .
  • Hibbett , D. S. , Pine , E. M. , Langer , E. , Langer , G. and Donoghue , M. J. 1997 . Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. . Proc. Natl. Acad. Sci. U.S.A. , 94 : 12002 – 12006 .
  • Hibbett , D. S. and Thorn , R. G. 2001 . “ Basidiomycota: Homobasidiomycetes. In: The Mycota VII B ” . In Systematics and Evolution. 121 – 168 . Berlin : Springer-Verlag . D.J. McLaughlin, E.G. McLaughlin & P.A. Lemke
  • Hirt , R. P. , John , J. , Logsdon , M. , Healy , B. , Dorey , M. W. , Doolittle , W. F. and Embley , T. M. 1999 . Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. . Proc. Natl. Acad. Sci. U.S.A. , 96 : 580 – 585 .
  • Honda , D. , Yokochi , T. , Nakahara , T. , Raghukumar , S. , Nakagiri , A. , Schaumann , K. and Higashihara , T. 1999 . Molecular phylogeny of labyrinthulids and thrausto- chytrids based on the sequencing of 18S ribosomal RNA gene. . J. Euk. Microbiol. , 46 : 637 – 47 .
  • Hudspeth , D. S.S. , Nadler , S. A. and Huspet , M. E. 2000 . A COX molecular phylogeny of the Peronosporomycetes. . Mycologia , 92 : 674 – 684 .
  • James , T. Y. , Porter , D. , Leander , C. A. , Vilgalys , R. and Longcore , J. E. 2000 . Molecular phylogenetics of the Chytridiomycota support the utility of ultrastructural data in chytrid systematics. . Can. J. Bot. , 78 : 336 – 350 .
  • Jensen , A. B. , Gargas , A. , Eilenberg , J. and Rosendahl , S. 1998 . Relationship of the insect-pathogenic order Entomophthorales (Zygomycota, Fungi) based on the phylogenetic analyses of the nuclear small subunit ribosomal DNA sequences (SSU rDNA). . Fungal Genet. Biol. , 24 : 325 – 334 .
  • Keeling , P. J. , Luker , M. A. and Palmer , J. D. 2000 . Evidence from beta-tubulin phylogeny that Microsporidia evolved from within the fungi. . Mol. Biol. Evoi , 17 : 23 – 31 .
  • Krüger , D. , Binder , M. , Fischer , M. and Kreisel , H. 2001 . The Lycoperdales. A molecular approach to the systematics of the gasteroid mushrooms. . Mycologia , 93 : 947 – 957 .
  • Lamarck , J. B. de . 1777–78 . Flore française ou description succincte de toutes les plantes qui croissent naturellement en France, disposées suivant une nouvelle méthode d'analyse… (3 vol.). Imp. Royale, Paris.
  • Lang , B. F. , Gray , M. W. and Burger , G. 1999 . Mitochondrial genome evolution and the origin of eukaryotes. . Ann. Rev. Genet. , 33 : 351 – 397 .
  • Lang , B. F. , Kelly , C. O. , Nerad , T. , Gray , M. W. and Burger , G. 2002 . The closest unicellular relatives of animals. . Curr. Biol. , 12 : 1773 – 1778 .
  • Lecointre , G. and Le Guyader , H. 2001 . Classification phy-logénétique du vivant. Belin, Paris 543
  • Leipe , D. D. , Wainright , P. , Gunderson , J. H. , Porter , D. , Patterson , D. J. , Valois , F. , Himmerich , S. and Sogin , M. L. 1994 . The stramenopiles from a molecular perspective: 16S like rRNA sequences from Labyrinthuloides minuta . Cafeteria roenbergensis. Phycologia , 33 : 369 – 377 .
  • Linné , C. von . 1738 . Classes plantarum. C. Wishoff, Lugduni Batavorum.
  • Liu , Y. J. , Whelen , S. and Hall , B. D. 1999 . Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. . Mol. Biol. Evol. , 16 : 1799 – 1808 .
  • Lumbsch , H. T. , Wirtz , N. , Lindemuth , R. and Schmitt , I. 2002 . Higher level phylogenetic relationships of Euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data. . Mycol. Prog. , 1 : 57 – 70 .
  • Martin , M. P. and Raccabruna , A. 1999 . The taxonomic boundaries between Naucoria rheophylla, Setchelliogaster tenuipes based on morphology and molecular data. . Mycotaxon , 71 : 141 – 148 .
  • Mendoza , L. , Taylor , J. W. and Ajello , L. 2002 . The class Mesomycetozoa: an heterogenous group of microorganisms at the animal-fungal boundary. . Ann. Rev. Microbiol. , 56 : 315 – 344 .
  • Moncalvo , J. M. , Lutzoni , F. M. , Rehner , S. A. , Johnson , J. and Vilgalys , R. 2000 . Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. . Syst. Biol. , 49 : 278 – 305 .
  • Moncalvo , J. M. , Vilgalys , R. , Redhead , S. A. , Johnson , J. E. , James , T. Y. , Aime , M. C. , Hofstetten , V. , Verduin , S. J.W. , Larsson , E. , Baroni , T. J. , Thorn , R. G. , Jacobsson , S. , Clémençon , H. and Miller , O. K. Jr. 2002 . One hundred and seventeen clades of Euagarics. . Mol. Phyl. Evoi , 23 : 357 – 400 .
  • Nagahama , T. , Sato , H. , Shimazu , M. and Sugiyama , J. 1995 . Phylogenetic divergence of the entomophtho- ralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences. . Mycologia , 87 : 203 – 209 .
  • Nishida , H. and Sygiyama , J. 1994 . Archiascomycetes: detection of a major new lineage within the ascomy- cota. . Mycoscience , 35 : 361 – 366 .
  • O'Donnell , K. , Cigelnik , E. and Benny , G. L. 1998 . Phylogenetic relationships among the Harpellales (Trichomycetes) and Kickxellales (Zygomycetes), two orders of Zygomycota that form regularly septate hyphae. . Mycologia , 90 : 624 – 639 .
  • O'Donnell , K. , Cigelnik , E. , Weber , N. S. and Trappe , J. M. 1997 . Phylogenetic relationships among ascomyce- tous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis. . Mycologia , 89 : 48 – 65 .
  • O'Donnell , K. , Lutzoni , F. M. , Ward , T. J. and Benny , G. L. 2001 . Evolutionary relationships among mucoralean fungi (Zygomycota): evidence for family polyphyly on a large scale. . Mycologia , 93 : 286 – 296 .
  • Peintner , U. , Bougher , N. L. , Castellano , M. A. , Moncalvo , J. M. , Moser , M. M. , Trappe , J. M. and Vilgalys , R. 2001 . Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae). . Am. J. Bot. , 88 : 2168 – 2179 .
  • Pine , E. M. , Hibbett , D. S. and Donoghue , M. J. 1999 . Phylogenetic relationships of cantharelloid and clava- rioid homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. . Mycologia , 91 : 944 – 963 .
  • Ragan , M. A. , Goggin , C. L. , Cawthorn , R. J. , Cerenius , L. , Jamieson , A. V.C. , Plourde , S. M. , Rand , T. G. , Söderhäll , K. and Gutell , R. R. 1996 . A novel clade of protis- tan parasites near the animal-fungal divergence . Proc. Natl. Acad. Sci. U.S.A. , 93 : 11907 – 11912 .
  • Redecker , D. , Morton , J. B. and Bruns , T. D. 2000 . Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). . Mol. Phyl. Evol. , 14 : 276 – 284 .
  • Roger , A. J. , Smith , M. W. , Doolittle , R. F. and Doolittle , W. F. 1996 . Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3- phosphate dehydrogenase. . J. Euk. Microbiol. , 43 : 475 – 485 .
  • Roux , C. , Almaraz , T. and Durrieu , G. 1998 . Phylogénie des champignons responsables des charbons des végétaux à partir de l'analyse des séquences ITS. . C. R. Acad. Sciences Paris , 321 : 603 – 609 . Sci. de la Vie
  • Schüßler , A. , Schwarzott , D. and Walker , C. 2001 . A new fungal phylum, the Glomeromycota: phylogeny and evolution. . Mycol. Res. , 105 : 1413 – 1421 .
  • Selosse , M. A. 2001 . La classification des Eucaryotes: un document de travail. . Bull. Soc. Fr. Syst. , 26 : 32 – 44 .
  • Selosse , M. A. , Weiß , M. , Jany , J. L. and Tillier , A. 2002 . Communities and populations of sebacinoid basidio- mycetes associated with the achlorophyllous orchid Neottia nidus-avis (L.) L.C.M. Rich, and neighbouring tree ectomycorrhizae. . Mol. Ecol. , 11 : 1831 – 1844 .
  • Simpson , A. G.B. and Roger , A. J. 2002 . Eukaryotic evolution: getting to the root of the problem. . Curr. Biol. , 12 : R691 – R693 .
  • Solignac , M. , Périquet , G. , Anxolabéhère , D. and Petit , C. 1995 . Génétique et évolution (tome 2): l'espèce, l'évolution moléculaire. Hermann, Paris 367
  • Stiller , J. W. and Hall , B. D. 1999 . Long-branch attraction and the rDNA model of early eukaryotic evolution. . Mol. Biol. Evol. , 16 : 1270 – 1279 .
  • Swann , E. C. , Frieders , E. M. and McLaughlin , D. J. 2001 . “ Urediniomycetes. In: The Mycota VII B ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 37 – 56 . Berlin : Springer-Verlag .
  • Swann , E. C. and Taylor , J. W. 1995a . Phylogenetic diversity of yeast-producing basidiomycetes. . Mycol. Res. , 99 : 1205 – 1210 .
  • Swann , E. C. and Taylor , J. W. 1995b . Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. . Can. J. Bot. , 73 : S862 S868
  • Swann , E. C. and Taylor , J. W. 1995c . Toward a phylogenetic systematics of the Basidiomycota: integrating yeasts and filamentous basidiomycetes using 18S RRNA gene sequences. . Studies in Mycology , 73 : 147 – 161 .
  • Tanabe , Y. , Watanabe , M. M. and Sugiyama , J. 2002 . Are Microsporidia related to fungi? A reappraisal based on additional gene sequences from basal fungi. . Mycol. Res. , 106 : 1380 – 1391 .
  • Tehler , A. , Farris , J. S. , Lipscomb , D. L. and Källersjo , M. 2000 . Phylogenetic analyses of the fungi based on large rDNA data sets. . Mycologia , 92 : 459 – 474 .
  • Tehler , A. , Little , D. P. and Farris , J. S. 2003 . The full-length phylogenetic trees from 1551 ribosomal sequences of chitinous fungi . Fungi. Mycol. Res. , 107 : 901 – 916 .
  • Thorn , R. G. , Moncalvo , J. M. , Reddy , C. A. and Vilgalys , R. 2000 . Phylogenetic analyses and the distribution of nemotaphagy support a monophyletic Pleurotaceae within polyphyletic pleurotoid-lentinoid fungi. . Mycologia , 92 : 241 – 252 .
  • Vandenkoornhuyse , P. , Baldauf , S. L. , Leyval , C. , Straczek , J. and Young , J. P.W. 2002 . Extensive fungal diversity in plant roots. . Science , 295 : 2051
  • Van der Auwera , G. , De Baere , R. , Van de Peer , Y. , De Rijk , P. , Van den Broeck , I. and De Wächter , R. 1995 . The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of . Hyphochytrium catenoides. Mol. Biol. Evol. , 12 : 671 – 678 .
  • Van't Klooster , J. W. , van den Berg-Velthuis , G. , van West , P. and Govers , F. 2000 . Gene , 249 : 145 – 151 . tef1, a Phytophthora infes- tans gene encoding translation elongation factor 1 alpha
  • Voigt , K. and Wöstemeyer , J. 2001 . Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF- 1 genes. . Gene , 270 : 113 – 120 .
  • Wainright , P. O. , Hinkle , G. , Sogin , M. L. and Stickel , S. K. 1993 . Monophyletic origins of the metazoa: an evolutionary link with fungi. . Science , 260 : 340 – 342 .
  • Wells , K. and Bandoni , R. 2001 . “ Heterobasidiomycetes. In: The Mycota VII B ” . In Systematics and Evolution. Edited by: McLaughlin , D. J. , McLaughlin , E. G. and Lemke , P. A. 85 – 120 . Berlin : Springer-Verlag .
  • Weiß , M. and Oberwinkler , F. 2001 . Phylogenetic relationships in Auriculariales and related groups; hypotheses derived from nuclear ribosomal DNA sequences. . Mycological Research , 105 : 403 – 415 .
  • Weiß , M. , Selosse , M. A. , Rexer , K. H. , Urban , A. and Oberwinkler , F. 2003 . “ Phylogenetic and ecological aspects of Sebacinales ord. nov., heterobasidiomycetes with a broad mycorrhizal potential. Soumis à ” . In Mycologia.
  • White , M. , Cafaro , M. and Lichtwardt , R. 2003 . “ What are fungi? Molecular data reveals phylogenetic surprises among the Trichomycetes (Zygomycotina). ” . In In: Résumés du IVe Halifax : International Symbiosis Society Congress . (août 2003), 118
  • Yoon , H. S. , Hackett , J. D. , Pinto , G. and Bhattacharya , D. 2002 . The single, ancient origin of chromist plastids. . Proc. Natl. Acad. Sci. U.S.A. , 99 : 15507 – 15512 .

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