Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota)

Genetica

Volumn 143, Issue 2, 2015, Pages 169-194

  Bellanger, J M ^a   Moreau, P A ^b   Corriol, G ^c   Bidaud, A ^d   Chalange, R ^d   Dudova, Z ^e   Richard, F ^f  

^a INSERM   (France)

^b UFR3S Pharmacie   (France)

^c Conservatoire botanique national des Pyrénées et de Midi Pyrénées ^*  (France)

^d Charles University ^*  (France)

^e CHARLES UNIVERSITY   (Czech Republic)

^f UNIV MONTPELLIER   (France)

Author keywords

Barcoding; Lyophyllaceae; Phylogeny; Species limits

Indexed keywords

FUNGAL DNA; FUNGAL PROTEIN; GENETIC MARKER; RIBOSOMAL SPACER DNA; RNA 5.8S; RNA POLYMERASE II;

AGARICALES; CLASSIFICATION; DNA BARCODING; GENETIC MARKER; GENETICS; PHYLOGENY; PROCEDURES;

AGARICALES; DNA BARCODING, TAXONOMIC; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; FUNGAL PROTEINS; GENETIC MARKERS; PHYLOGENY; RNA POLYMERASE II; RNA, RIBOSOMAL, 5.8S;

EID: 84925496014     PISSN: 00166707     EISSN: 15736857     Source Type: Journal    
DOI: 10.1007/s10709-015-9823-8     Document Type: Article

References (56)

1. Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S et al (2010) The UNITE database for molecular identification of fungi—recent updates and future perspectives. New Phytol 186(2):281–285
2. Alvarado P, Moreno G, Vizzini A, Consiglio G, Manjón JL, Setti L (2014) Atractosporocybe, Leucocybe and Rhizocybe: three new clitocyboid genera in the Tricholomatoid clade (Agaricales) with notes on Clitocybe and Lepista. Mycologia 106(5):13–369
3. Anisimova M, Gil M, Dufayard J-F, Dessimoz C, Gascuel O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60(5):685–699
4. Baroni TJ, Franco-Molano AE, Lodge J, Linder DL, Horak E, Hofstetter V (2007) Arthromyces and Blastosporella, two new genera of conidia-producing lyophylloid agarics (Agaricales, Basidiomycota) from the neotropics. Mycol Res 111:572–580
5. Bon, M. (1992) Clé monographique des espèces galéro-naucorioïdes. Association d’écologie et de mycologie
6. Bon M (1994) Deux Lyophylloideae intéressantes et le genre Gerhardtia st. et nom. nov. Doc Mycol 24(93):65–68
7. Bon M (1999). Flore mycologique d’Europe 5. Collybio-marasmioïdes et ressemblants. Documents Mycologiques, Mémoire hors série n°5. Lille
8. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4):540–552
9. Chevenet F, Brun C, Bañuls A-L, Jacq B, Christen R (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinform 7:439
10. Consiglio G, Contu M (2002) Il genere Lyophyllum P. Karst. emend. Kühner, in Italia. Rivista di Micologia 45:99–181
11. Contu M, Consiglio G (2005) “2004” Il genere Gerhardtia (Lyophyllaceae) in Europa, con osservazioni sulle rimanenti specie conosciute. Micologia e Vegetazione Mediterranea 19(2): 151–162
12. Cooper JA (2014) New species and combinations of some New Zealand agarics belonging to Clitopilus, Lyophyllum, Gerhardtia, Clitocybe, Hydnangium, Mycena, Rhodocollybia and Gerronema. Mycosphere 5(2):263–288
13. Courtecuisse R, Duhem B (2012) Champignons de France et d’Europe. 2e édition. Delachaux & Niestlé, Lausanne
14. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F et al (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36(2):465–469
15. Donk MA (1962) The generic names proposed for Agaricaceae. Beihefte zur Nova Hedwigia 5:320
16. Du X-H, Zhao Q, Yang ZL, Hansen K, Taşkın H, Büyükalaca S et al (2012) How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia 104:1351–1368
17. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
18. Frøslev TG, Jeppesen TS, Laessøe T, Kjøller R (2007) Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe. Mol Phylogenet Evol 44(1):217–227
19. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118
20. Giraud T, Refrégier G, Le Gac M, de Vienne DM, Hood ME (2008) Fungal Genet Biol 45(6):791–802
21. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al (2010) New algorithms and methods to estimate maximum likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321
22. Harder CB, Laessøe T, Frøslev TG, Ekelund F, Rosendhal S, Kjøller R (2013) A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification. Fungal Biol 117:764–775
23. Hibbett DS (2007) After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century. Mycol Res 111:1001–1018
24. Hofstetter V, Clémençon H, Vilgalys R, Moncalvo JM (2002) Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences. Mycol Res 106(9):1043–1059
25. Hofstetter V, Redhead SA, Kauff F, Moncalvo J-M, Matheny PB, Vilgalys R (2014) Taxonomic revision and examination of ecological transitions of the Lyophyllaceae (Basidiomycota, Agaricales) based on a multigene phylogeny. Cryptogam Mycol 35(4):399–425
26. Holec J, Kolařík M (2013) Ossicaulis lachnopus (Agaricales, Lyophyllaceae), a species similar to O. lignatilis, is verified by morphological and molecular methods. Mycol Prog 12(3):589–597
27. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ et al (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818–822
28. Jargeat P, Martos F, Carriconde F, Gryta H, Moreau P-A, Gardes M (2010) Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota). Mol Ecol 19:5216–5230
29. Jülich W (1982) Lyophyllaceae. Bibl Mycol 85:378
30. Karsten PA (1881) Hymenomycetes Fennici. Acta Societatis pro Fauna et Flora Fennica 2(1):40
31. Kiss L (2012) Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad Sci USA 109(27):E1811
32. Knudsen H, Vesterholt J, (eds) (2012) Funga Nordica. Nordsvamp, Copenhagen
33. Kühner R (1938) Utilisation du carmin acétique dans la classification des Agarics leucosporés. Bulletin Mensuel de la Société Linnéenne de Lyon 7:204–211
34. Kühner R (1980) Les Hyménomycètes agaricoides. Bulletin Mensuel de la Société Linnéenne de Lyon 49:1–1027
35. Kühner R, Romagnesi H (1953) Flore analytique des champignons supérieurs (agarics, bolets, chanterelles). Masson & Cie, Paris
36. Larsson E, Sundberg H (2011) Lyophyllum shimeji, a species associated with lichen pine forest in northern Fennoscandia. Mycoscience 52(5):289–295
37. Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799–1808
38. Matheny PB (2005) Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe, Agaricales). Mol Phylogenet Evol 35:1–20
39. Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo JM, Ge ZW (2006) Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98(6):982–995
40. Moreau P-A, Vila J, Aime MC, Antonin V, Horak E, Pérez-Butron JL, Richard F, Urban A, Welti S, Vizzini A (2015) Cibaomyces and Cyptotrama, two new genera for Europe, and an emendation of Rhizomarasmius (Basidiomycota, Physalacriaceae). Mycol Prog (in press)
41. Neville P, Poumarat S (1997) Premiere récolte française de Tephrocybe gibberosa et sa position par rapport aux Tephrocybe carbonicoles. Bollettino del Gruppo Micologico Bresadola 40:347–366
42. Norvell LL (2010) Report of the nomenclature committee for fungi: 15. Taxon 59(1):291–293
43. O’Donnell K, Rooney AP, Mills GL, Kuo M, Weber NS, Rehner SA (2011) Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic. Fungal Genet Biol 48:252–265
44. Osmundson TW, Robert VA, Schoch CL, Baker LJ, Smith A, Robich G et al (2013) Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One 8(4):e62419
45. R Core Team (2014) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. http://www.R-project.org/
46. Redhead SA (1981) Parasitism of bryophytes by agarics. Can J Bot 59:63–67
47. Redhead SA (2014) Nomenclatural novelties. Index Fungorum 202:1
48. Redhead SA, Hofstetter V, Clémençon H, Moncalvo J-M (2006) 1742) Proposal to conserve the name Lyophyllum with a conserved type (Basidiomycota. Taxon 55(4):1034–1036
49. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574
50. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109(16):6241–6246
51. Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Res 9:83–89
52. Singer R (1986) The agaricales in modern taxonomy. Koeltz Scientific Books, Koenigstein, p 981p
53. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4):564–577
54. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31(1):21–32
55. Vesterholt J, Ludwig E (2012) Lyophyllum. In: Knudsen H, Vesterholt J, (eds): 583
56. Wang X-Q, Zhou D-Q, Zhao Y-C, Zhang X-L, Li L, Li S-H (2013) Lyophyllum rhombisporumsp. nov. from China. Mycotaxon 123(5):473–477