Phylogenetic analysis of Aspergillus species using DNA sequences from four loci

DNA sequences were determined for beta tubulin (BT2), calmodulin (CF), ITS and lsu rDNA (ID) and RNA polymerase II (RPB2) from ca. 460 Aspergillus isolates. RPB2 and rDNA sequences were combined and analyzed to determine relationships in the genus and in the family Trichocomaceae. Eupenicillium species form a statistically supported clade with origins among the Aspergillus clades. A. crystallinus, A. malodoratus and H. paradoxus are members of the Eupenicillium clade. A. zonatus, A. clavatoflvus and W. spinulosa occur in a clade along with Hamigera sp. Other than these exceptional species, Aspergillus species and sections occur on three strongly supported clades that descend from a polytomy. Section Versicolores as a monophyletic group includes only A. versicolor and A. sydowii and is superfluous. The other sections were retained but modified. All four loci were used in genealogical concordance analysis of species boundaries. Fennellia flavipes and F. nivea are not conspecific with their supposed anamorphs A. flavipes and A. nivea. Synonymies were found for some species and more than 20 undescribed taxa were identified in genealogical concordance analysis. Newly discovered taxa will be described elsewhere. Possibly paralogous gene fragments were amplified with the BT2 primers in sections Nidulantes, Usti and Nigri. Use of nonhomologous sequences in genealogical concordance analysis could lead to false conclusions and so BT2 sequences were not used in analysis of those sections.

[1]  O. Rieppel.  Species: kinds of individuals or individuals of a kind , 2007, Cladistics : the international journal of the Willi Hennig Society.

[2]  S. Peterson,et al.  Penicillium astrolabium and Penicillium neocrassum, two new species isolated from grapes and their phylogenetic placement in the P. olsonii and P. brevicompactum clade , 2007, Mycologia.

[3]  David M. Geiser,et al.  Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. , 2006, Mycologia.

[4]  D. Jacobson,et al.  Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex , 2006, Mycologia.

[5]  Armando Venâncio,et al.  Aspergillus ibericus: a new species of section Nigri isolated from grapes. , 2006, Mycologia.

[6]  J. Frisvad,et al.  Novel Neosartorya species isolated from soil in Korea. , 2006, International journal of systematic and evolutionary microbiology.

[7]  A. Logrieco,et al.  Ochratoxin A Production and Amplified Fragment Length Polymorphism Analysis of Aspergillus carbonarius, Aspergillus tubingensis, and Aspergillus niger Strains Isolated from Grapes in Italy , 2006, Applied and Environmental Microbiology.

[8]  J. Ito,et al.  Mistaken Identity: Neosartorya pseudofischeri and Its Anamorph Masquerading as Aspergillus fumigatus , 2005, Journal of Clinical Microbiology.

[9]  Christina A. Cuomo,et al.  Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae , 2005, Nature.

[10]  J. Frisvad,et al.  Polyphasic taxonomy of Aspergillus fumigatus and related species , 2005 .

[11]  J. Frisvad,et al.  Polyphasic taxonomy of Aspergillus fumigatus and related species. , 2005, Mycologia.

[12]  C. Kurtzman,et al.  Rapid Identification of Candida Species and Other Clinically Important Yeast Species by Flow Cytometry , 2005, Journal of Clinical Microbiology.

[13]  S. Kocsubé,et al.  Evolutionary Relationships Among Aspergillus terreus Isolates and their Relatives , 2005, Antonie van Leeuwenhoek.

[14]  J. Frisvad,et al.  Taxonomic comparison of three different groups of aflatoxin producers and a new efficient producer of aflatoxin B1, sterigmatocystin and 3-O-methylsterigmatocystin, Aspergillus rambellii sp. nov. , 2005, Systematic and applied microbiology.

[15]  T. Lott,et al.  Assessment of Ribosomal Large-Subunit D1-D2, Internal Transcribed Spacer 1, and Internal Transcribed Spacer 2 Regions as Targets for Molecular Identification of Medically Important Aspergillus Species , 2005, Journal of Clinical Microbiology.

[16]  S. Carroll,et al.  More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. , 2005, Molecular biology and evolution.

[17]  D. Nickle,et al.  Aspergillus lentulus sp. nov., a New Sibling Species of A. fumigatus , 2005, Eukaryotic Cell.

[18]  J. Frisvad,et al.  Emericella venezuelensis, a new species with stellate ascospores producing sterigmatocystin and aflatoxin B1. , 2004, Systematic and applied microbiology.

[19]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[20]  J. Logsdon.  Worm genomes hold the smoking guns of intron gain. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[21]  P. Naaber,et al.  Isolation of Neosartorya pseudofischeri from Blood: First Hint of Pulmonary Aspergillosis , 2004, Journal of Clinical Microbiology.

[22]  Jens Christian Frisvad,et al.  Phylogenetic analysis of Penicillium subgenus Penicillium using partial P-tubulin sequences , 2004 .

[23]  J. Frisvad,et al.  New ochratoxin A producing species of Aspergillus section Circumdati , 2004 .

[24]  Jens Christian Frisvad,et al.  New ochratoxin A or sclerotium producing species in Aspergillus section Nigri. , 2004 .

[25]  D. Jacobson,et al.  REPRODUCTIVE ISOLATION AND PHYLOGENETIC DIVERGENCE IN NEUROSPORA: COMPARING METHODS OF SPECIES RECOGNITION IN A MODEL EUKARYOTE , 2003, Evolution; international journal of organic evolution.

[26]  D. Jacobson,et al.  A MULTILOCUS GENEALOGICAL APPROACH TO PHYLOGENETIC SPECIES RECOGNITION IN THE MODEL EUKARYOTE NEUROSPORA , 2003, Evolution; international journal of organic evolution.

[27]  J. Sites,et al.  Delimiting species: a Renaissance issue in systematic biology , 2003 .

[28]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[29]  J. Guarro,et al.  Cerebral Aspergillosis Caused by Neosartorya hiratsukae, Brazil , 2002, Emerging infectious diseases.

[30]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[31]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[32]  N. B. Gusmão,et al.  Neosartorya takakii, a new species from soil in Brazil , 2001 .

[33]  J. Huelsenbeck,et al.  MRBAYES : Bayesian inference of phylogeny , 2001 .

[34]  D. Hibbett,et al.  Phylogenetic species recognition and species concepts in fungi. , 2000, Fungal genetics and biology : FG & B.

[35]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[36]  B. Hall,et al.  Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. , 1999, Molecular biology and evolution.

[37]  J. Sugiyama,et al.  Polyphyletic origins of species of the anamorphic genus Geosmithia and the relationships of the cleistothecial genera: Evidence from 18S, 5S and 28S rDNA sequence analyses , 1997 .

[38]  S. Lonial,et al.  Neosartorya fischeri: an invasive fungal pathogen in an allogeneic bone marrow transplant patient , 1997, Bone Marrow Transplantation.

[39]  S. Peterson.  Phylogenetic analysis of Aspergillus sections Cremei and Wentii, based on ribosomal DNA sequences , 1995 .

[40]  N. L. Glass,et al.  Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes , 1995, Applied and environmental microbiology.

[41]  J. Sugiyama,et al.  Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S, 5.8S and ITS ribosomal DNA sequence data. , 1995 .

[42]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[43]  A. Padhye,et al.  Osteomyelitis caused by Neosartorya pseudofischeri , 1994, Journal of clinical microbiology.

[44]  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 .

[45]  J. Pitt,et al.  Infrageneric Taxa of Aspergillus , 1986 .

[46]  J. Pitt.  The genus Penicillium and its teleomorphic states Eupenicillium and Talaromyces , 1981 .

[47]  R. Samson.  A compilation of the aspergilli described since 1965 , 1979 .

[48]  E. G. Simmons,et al.  New Species and a New Genus of Plectomycetes with Aspergillus States , 1973 .

[49]  D. I. Fennell,et al.  ASCOCARPS OF ASPERGILLUS STROMATOIDES, A. NIVEUS, AND A. FLAVIPES- , 1973 .

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

[51]  G. Smith.  A Manual of the Aspergilli , 1946, Nature.

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

[53]  The Aspergilli , 1927, Nature.