One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR

Some fungi with pleomorphic life-cycles still bear two names despite more than 20 years of molecular phylogenetics that have shown how to merge the two systems of classification, the asexual “Deuteromycota” and the sexual “Eumycota”. Mycologists have begun to flout nomenclatorial regulations and use just one name for one fungus. The International Code of Botanical Nomenclature (ICBN) must change to accommodate current practice or become irrelevant. The fundamental difference in the size of fungi and plants had a role in the origin of dual nomenclature and continues to hinder the development of an ICBN that fully accommodates microscopic fungi. A nomenclatorial crisis also looms due to environmental sequencing, which suggests that most fungi will have to be named without a physical specimen. Mycology may need to break from the ICBN and create a MycoCode to account for fungi known only from environmental nucleic acid sequence (i.e. ENAS fungi).

[1]  J. Frisvad,et al.  Taxonomy of Penicillium citrinum and related species , 2010, Fungal Diversity.

[2]  D. Reynolds,et al.  Article 59 : reinterpretation or revision , 1992 .

[3]  George M. Garrity,et al.  Draft BioCode 2011: principles and rules regulating the naming of organisms. , 2011 .

[4]  P. A. Saccardo,et al.  Sylloge fungorum omnium hucusque cognitorum. Digessit P. A. Saccardo. , 1882 .

[5]  M. Berbee,et al.  18S Ribosomal RNA gene sequence characters place the human pathogenSporothrix schenckii in the genusOphiostoma , 1992 .

[6]  D. Reynolds,et al.  The fungal holomorph : mitotic, meiotic and pleomorphic speciation in fungal systematics : proceedings of an International Symposium, Newport, Oregon, 4-7 August, 1992 , 1993 .

[7]  W. Hennig.  Phylogenetic Systematics , 2002 .

[8]  R. Henrik Nilsson,et al.  Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences , 2011 .

[9]  Thomas D. Bruns,et al.  Fungal Molecular Systematics , 1991 .

[10]  A. Burt,et al.  Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Possession, use, and transfer of select agents and toxins. Final rule. , 2005, Federal register.

[12]  J. Townsend,et al.  Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[13]  Systematics of basidiomycetes based on 5S rRNA sequences and other data , 1983, Nature.

[14]  T. White.  Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics , 1990 .

[15]  K. Jones,et al.  Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. , 2010, The New phytologist.

[16]  John W. Taylor,et al.  Making the Deuteromycota redundant: a practical integration of mitosporic and meiosporic fungi , 1995 .

[17]  C. Kurtzman,et al.  Two New and Closely Related Heterothallic Species, Pichia amylophila and Pichia mississippiensis: Characterization by , 1980 .

[18]  Seung-Beom Hong,et al.  The Amsterdam Declaration on Fungal Nomenclature , 2011, IMA fungus.

[19]  A. Burt,et al.  Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Kevin D. Hyde,et al.  (117-119) Proposals to make the pre-publication deposit of key nomenclatural information in a recognized repository a requirement for valid publication of organisms treated as fungi under the Code , 2010 .

[21]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[22]  C. Kurtzman,et al.  Evolutionary Affinities of Heterobasidiomycetous Yeasts Estimated from 18S and 25S Ribosomal RNA Sequence Divergence , 1989 .

[23]  Paul Rabinow,et al.  Making PCR: A Story of Biotechnology , 1997 .

[24]  W. Marasas,et al.  Phylogenetic lineages in the Botryosphaeriaceae , 2006, Studies in mycology.

[25]  R. Petersen,et al.  IMC9 Edinburgh Nomenclature Sessions , 2010, IMA fungus.

[26]  R. Samson,et al.  Patterns of development in conidial fungi , 1980 .

[27]  J. Palmer,et al.  Accelerated evolution of a false-truffle from a mushroom ancestor , 1989, Nature.

[28]  K. Raper,et al.  The genus Aspergillus , 1966 .

[29]  R. Shoemaker,et al.  Systematics and mating systems of two fungal pathogens of opium poppy: the heterothallic Crivellia papaveracea with a Brachycladium penicillatum asexual state and a homothallic species with a Brachycladium papaveris asexual state , 2006 .

[30]  W. Doolittle,et al.  Redividing the basidiomycetes on the basis of 5S rRNA sequences , 1982, Nature.

[31]  J. Lafay,et al.  Phylogeny of some Fusarium species, as determined by large-subunit rRNA sequence comparison. , 1989, Molecular biology and evolution.

[32]  D. Reynolds,et al.  DNA specimens and the 'International code of botanical nomenclature' , 1991 .

[33]  G. F. Smith,et al.  Did Scott typify names in Haworthia (Asphodelaceae: Alooideae)? , 1993 .

[34]  S. J. Hughes.  CONIDIOPHORES, CONIDIA, AND CLASSIFICATION , 1953 .

[35]  P. A. Saccardo.  Sylloge fungorum omnium hucusque cognitorum. , 1882 .

[36]  G. Martin.  The Genus Aspergillus. , 1946, Science.

[37]  Karl Wilhelm Gottlieb Leopold Fuckel.  Symbolae mycologicae : Beiträge zur Kenntniss der Rheinischen Pilze , 1869 .

[38]  K. Jones,et al.  Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. , 2009, The New phytologist.

[39]  B. Kendrick.  The Whole Fungus: The Sexual-Asexual Synthesis , 1979 .

[40]  T. White,et al.  Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis , 2002, Mycologia.

[41]  P. Crous,et al.  (016-020) Proposals to amend the Code to make clear that it covers the nomenclature of fungi, and to modify its governance with respect to names of organisms treated as fungi , 2009 .

[42]  G. Barron.  The genera of Hyphomycetes from soil. , 1968 .

[43]  F. Pineau,et al.  Carbon geodynamic cycle (reply) , 1983, Nature.