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Molecular Evoloution and Systematics

Phylogenetic assessment of Chromocyphellaceae (Agaricineae, Basidiomycota) and a new lamellate species of Chromocyphella

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Pages 578-587 | Received 09 Mar 2017, Accepted 18 Aug 2017, Published online: 11 Oct 2017

LITERATURE CITED

  • Binder M, Larsson KH, Matheny PB, Hibbett DS. 2010. Amylocorticiales ord. nov. and Jaapiales ord. nov.: early-diverging clades of Agaricomycetidae dominated by corticioid forms. Mycologia 102:865–880.
  • Bodensteiner P, Binder M, Moncalvo J-M, Agerer R, Hibbett DS. 2004. Phylogenetic relationships of cyphelloid homobasidiomycetes. Molecular Phylogenetics and Evolution 33:501–515.
  • Clarke D. 2014. Notes on the bryophilous fungus Chromocyphella muscicola (Fr.) Donk in Cumbria. Lakeland Naturalist 2:24–28.
  • Dentinger BTM, Gaya E, O’Brien H, Suz LM, Lachlan R, Díaz-Valderrama JR, Koch RA, Aime MC. 2016. Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life. Biological Journal of the Linnean Society 117:11–32.
  • Doassans E, Patouillard NT. 1886. Champignons de Béarn (2e liste). Revue Mycologique (Toulouse) 8(29):25–28.
  • Donk MA. 1959. Notes on “Cyphellaceae”. Persoonia 1:25–110.
  • Donk MA. 1966. A reassessment of the Cyphellaceae. Acta Botanica Neerlandica 15:95–101.
  • Dore J, Perraud M, Dieryckx C, Kohler A, Morin E, Henrissat B, Lindquist E, Zimmermann SD, Girard V, Kuo A, Grigoriev IV, Martin F, Marmeisse R, Gay G. 2015. Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytologist 208:1169–1187.
  • Garnica S, Weiss M, Walther G, Oberwinkler F. 2007. Reconstructing the evolution of agarics from nuclear gene sequences and basidiospore ultrastructure. Mycological Research 111:1019–1029.
  • Hansen K, Pfister DH, Hibbett DS. 1999. Phylogenetic relationships among species of Phillipsia inferred from molecular and morphological data. Mycologia 91:299–314.
  • Heinemann P, Rammeloo J. 1985. De la mesure des spores et de son expression. Agarica 6:366–380.
  • Hesler LR, Smith AA. 1965. The North American species of Crepidotus. New York and London: Hafner Publishing Company. 126 p.
  • Hildén K, Mäkelä MR, Steffen KT, Hofrichter M, Hatakka A, Archer DB, Lundell TK. 2014. Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox. Fungal Genetics and Biology 72:131–136.
  • Horak E. 1978. Pleuroflammula. Persoonia 9:439–451.
  • Horak E. 1989. New and additional data concerning Pyrrhoglossum and eccentric or laterally stipitate taxa of Gymnopilus (Agaricales). Opera Botanica. 100:115–129.
  • Jacobsson S. 2008. Flammula. In: Knudsen H, Vesterholt J, eds. Funga Nordica. Copenhaghen, Denmark: Nordsvamp. p. 785–787.
  • Kirk P, Cannon PF, Minter DW, Stalpers JA. 2008. The dictionary of fungi. 10th ed. Wallingford, UK: CAB International. 784 p.
  • Knudsen H, Vesterholt J. 2012. Funga Nordica. 2nd revised and augmented edition. 2 volumes. Copenhagen, Denmark: Nordsvamp. 1083 p.
  • Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja H-R, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Mycorrhizal Genomics Initiative Consortium, Tunlid A, Grigoriev IV, Hibbett DS, Martin F. 2015. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics 47:410–415.
  • Larsson A. 2014. AliView: a fast and lightweight alignment viewer and editor for large data sets. Bioinformatics 30:3276–3278.
  • Mason-Gamer RJ, Kellogg EA. 1996. Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Graminaeae). Systematics and Biology 45:524–545.
  • Martin F, Aerts A, Ahr D, Brun A, Danchin EGJ, Duchaussoy F, Gibon J, Kohler A, Lindquist E, Pereda V, Salamov A, Shapiro HJ, Wuyts J, Blaudez D, Bu M, Brokstein P, Canb B, Cohen D, Courty PE, Coutinho PM, Delaruelle C, Detter JC, Deveau A, DiFazio S, Duplessis S, Fraissinet-Tachet L, Lucic E, Frey-Klett P, Fourrey C, Feussner I, Gay G, Grimwood J, Hoegger PJ, Jain P, Kilaru S, Labb J, Y. C. Lin5, Legu V, Le Tacon F, Marmeisse R, Melayah D, Montanini B, Muratet M, Nehls U, Niculita-Hirzel H, Oudot-Le Secq MP, Peter M, Quesneville H, Rajashekar B, Reich M, Rouhier N, Schmutz J, Yin T, Chalot M, Henrissat B, Lucas S, Van de Peer Y, Podila GK, Polle A, Pukkila PJ, Richardson PM, Rouz P, Sanders IR, Stajich JE, Tunlid A, Tuskan G, Grigoriev IV 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92.
  • Matheny PB, Hofstetter V, Aime MC, Moncalvo JM, Ge Z-W, Yang Z-L, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. 2006. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982–995.
  • Matheny PB, Liu JY, Ammirati J, Hall BD. 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). American Journal of Botany 89:688–698.
  • Matheny PB, Moreu P-A, Vizzini A, Harrower E, De Haan A, Contu M, Curti M. 2014. Crassisporium and Romagnesiella: two new genera of dark-spored Agaricales. Systematics and Biodiversity 13:28–41.
  • Matheny PB, Vellinga EC, Bougher N, Ceska O, Moreau P-A, Neves MA, Ammirati J 2007. Taxonomy of displaced species of Tubaria. Mycologia 99:569–585.
  • Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop (GCE), New Orleans, LA, 14 November 2010, p. 1–8.
  • Moncalvo J-M, Vilgalys R, Redhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clémençon H, Miller OK Jr. 2002. One hundred and seventeen clades of euagarics. Molecular Phylogenetics and Evolution 23:357–400.
  • Moreno G, Castillo A. 2013. A comparative study of the types of three species of Myxomycetes: Trichia crateriformis, T. fallax var. olivacea and T. fernbankensis. Boletín de la Sociedad Micológica de Madrid 37:85–98.
  • Patouillard NT. 1886. Tabulae analyticae fungorum. Fasc. 5. Poligny, France: Librairie C. Klincksieck.
  • Petersen G, Knudsen H, Seberg O. 2010. Alignment, clade robustness and fungal phylogenetics—Crepidotaceae and sister families revisited. Cladistics 26:62–71.
  • Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v. 1.6. [cited 2016 Jul 30]. Available from: http://beast.bio.ed.ac.uk/Tracer
  • Rees BJ, Zuccarello GC, Orlovich DA. 2002. Relationships between Australian and Northern hemisphere Gymnopilus species II. A preliminary phylogeny of species of Gymnopilus and related genera based on internal transcribed spacer (ITS) region of ribosomal DNA. Mycotaxon 84:93–110.
  • Rehner S, Buckley E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84–98.
  • Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. 2014. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proceedings of the National Academy of Sciences of the United States of America 111:9923–9928.
  • Ronquist F, Teslenko M, Mark P van der, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539–542.
  • Salom JC, Esteve-Raventós F. 2011. Phaeomarasmius siquierii (Agaricoid clade, Tubariaceae), a new Mediterranean resupinate species found in Formentera (Balearic Islands, Spain). Micologia e Vegetazione Mediterranea 26:29–36.
  • Senn-Irlet B. 2008. Chromocyphella. In: Knudsen H, Vesterholt J, eds. Funga Nordica. Copenhaghen, Denmark: Nordsvamp. p. 861–863.
  • Singer R. 1944. New genera of fungi. Mycologia 36:358–368.
  • Stafleu FA, Cowan RS. 1983. Taxonomic literature 4. P-Sak. Utrecht, the Netherlands: Bohn, Scheltema & Holkema. 1214 p.
  • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.
  • Stiller JW, Hall BD. 1997. The origin of red algae: implications for plastid evolution. Proceedings of the National Academy of Sciences of the United States of America 94:4520–4525.
  • Sulzbacher MA, Coelho G, Cortez VG. 2009. Studies on cyphelloid fungi in Southern Brazil. The genus Phaeosolenia Speg. Boletín de la Sociedad Micológica de Madrid 33:91–96.
  • Thiers B. 2012 (continuously updated). Index herbariorum. A global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. [ cited 2013 Feb 26]. Available from: http://sweetgum.nybg. org/ih/
  • Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172:4238–4246.
  • White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Inns MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. San Diego, California: Academic Press. p. 315–322.

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