Phylogenetic analysis of Aspergillus species using DNA sequences from four loci

Mycologia

Volumn 100, Issue 2, 2008, Pages 205-226

  Peterson, Stephen W ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

Aspergillus brevijanus comb. nov.; Beta tubulin; Calmodulin; Concordance analysis; Dichotomomyces; RNA polymerase II; Talaromyces; Thermoascus; Trichocomaceae

Indexed keywords

ENZYME ACTIVITY; FUNGUS; GENETIC ANALYSIS; PHYLOGENY;

ASPERGILLUS; ASPERGILLUS CRYSTALLINUS; ASPERGILLUS FLAVIPES; ASPERGILLUS MALODORATUS; ASPERGILLUS SYDOWII; ASPERGILLUS VERSICOLOR; ASPERGILLUS ZONATUS; DICHOTOMOMYCES; EUPENICILLIUM; HAMIGERA; TALAROMYCES; THERMOASCUS; TRICHOCOMACEAE;

ARTICLE; ASPERGILLUS; CLASSIFICATION; DNA SEQUENCE; FUNGAL GENE; GENETICS; MOLECULAR GENETICS; PHYLOGENY;

ASPERGILLUS; GENES, FUNGAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 48249119613     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/mycologia.100.2.205     Document Type: Article

References (53)

1. Balajee SA, Gribskov J, Brandt M, Ito J, Fothergill A, Marr KA. 2005a. Mistaken identity: Neosartorya pseudofischeri and its anamorph masquerading as Aspergillus fumigatus. J Clin Microbiol 43:5996-5999.
2. -, -, Hanley D, Nickle D, Marr KA. 2005b. Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus. Eukaryot Cell 4:625-632.
3. Baum DA, Shaw KL. 1995. Genealogical perspectives on the species problem. In: Hoch PC, Stephenson AG, eds. Experimental and Molecular Approaches to Plant Biosystematics Missouri Botanical Garden. p 289-303.
4. Berbee ML, Yoshimura A, Sugiyama J, Taylor JW. 1995. Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S, 5.8S and ITS ribosomal DNA sequence data. Mycologia 87:210-222.
5. Dettman JR, Jacobson DJ, Taylor JW. 2003a. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57:2703-2720.
6. -, -, Turner E, Pringle A, Taylor JW. 2003b. Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model Eukaryote. Evolution 57:2721-2741.
7. -, -, Taylor JW. 2006. Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex. Mycologia 98:436- 446.
8. Frisvad JC, Frank JM, Houbraken JAMP, Kuijpers AFA, Samson RA. 2004. New ochratoxin A producing species of Aspergillus section Circumdati. Stud Mycol 50:23-43.
9. -, Samson RA. 2004. Emericella venezuelensis, a new species with stellate ascospores producing sterigmatocystin and aflatoxin B1. Syst Appl Microbiol 27:672- 680.
10. -, Skouboe P, Samson RA. 2005. Taxonomic comparison of three different groups of aflatoxin producers and a new efficient producer of aflatoxin B1, sterigmatocystin and 3-O-methylsterigmatocystin, Aspergillus rambelli sp. nov. Syst Appl Microbiol 28:442-453.
11. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Bastürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW. 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1092-1093.
12. Gams W, Christensen M, Onions AHS, Pitt JI, Samson RA. 1985. Infrageneric taxa of Aspergillus. In: Samson RA, Pitt JI, eds. Advances in Aspergillus systematics. New York: Plenum Press. p 55-64.
13. Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, Hofstetter V, Fraker E, Schoch CL, Tibell L, Untereiner WA, Aptroot A. 2006. Eurotiomycetes: Eurotiomycetidae and Caetothyriomycetidae. Mycologia 98:1053- 1064.
14. Glass NL, Donaldson G. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323-1330.
15. Guarro J, Kallas EG, Godoy P, Karenina A, Gene J, Stchigel A, Colombo AL. 2002. Cerebral apergillosis caused by Neosartorya hiratsukae, Brazil. Emerging Infect Dis 8: 989-991.
16. Hinrikson HP, Hurst SF, Lott TJ, Warnock DW, Morrison CJ. 2005. 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. J Clin Microbiol 43:2092-2103.
17. Hong S-B, Go S-J, Shin H-D, Frisvad JC, Samson RA. 2005. Polyphasic taxonomy of Aspergillus fumigatus and related species. Mycologia 97:1316-1329.
18. -, Cho H-S, Shin H-D, Frisvad JC, Samson RA. 2006. Novel Neosartorya species isolated from soil in Korea. Int J Syst Evol Microbiol 56:477-486.
19. Horie Y, Makoto M, Nishimura K, Franco MF, Coelho KIR. 1995. New and interesting species of Neosartorya from Brazilian soil. Mycoscience 36:199-204.
20. -, Abliz P, Fukushina K, Okada K, Gusmao NB. 2001. Neosartorya takakii, a new species from soil in Brazil. Mycoscience 42:91-95.
21. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
22. Jarv H, Lehtmaa J, Summerbell RC, Hoekstra ES, Samson RA, Naaber P. 2004. Isolation of Neosartorya fischeri from blood: first hint of pulmonary aspergillosis. J Clin Microbiol 42:925-928.
23. Liu Y, Whelen S, Hall BD. 1999. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16:1799-1808.
24. LoBuglio KF, Taylor JW. 1993. Molecular phylogeny of Talaromyces and Penicillium species in subgenus Biverticillium. In: Reynolds DR, Taylor JW, eds. The fungal holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics. Surrey, UK: CAB International. p 115-119.
25. Logsdon JM. 2004. Worm genomes hold the smoking guns of intron gain. Proc Nat Acad Sci (USA) 101:11195- 11196.
26. Lonial S, Williams L, Carrum G, Ostrowski M, McCarthy P. 1997. Neosartorya fischeri: an invasive fungal pathogen
27. in an allogeneic bone marrow transplant patient. Bone Marrow Transplant 19:753-755.
28. Ogawa H, Yoshimura A, Sugiyama J. 1997. Polyphyletic origins of species of the anamorphic genus Geosmithia and the relationships of the cleistothecial genera: evidence from 18S, 5S and 28S rDNA sequence analysis. Mycologia 89:756-771.
29. Padhye AA, Godfrey JH, Chandler FW, Peterson SW. 1995. Osteomyelitis caused by Neosartorya pseudofischeri. J Clin Microbiol 32:2832-2836.
30. Page BT, Kurtzman CP. 2005. Rapid identification of Candida species and other clinically important yeast species by flow cytometry. J Clin Microbiol 43:4507- 4514.
31. Perrone G, Mulè G, Susca A, Battilani P, Pietri A, Logrieco A. 2006. Ochratoxin A production and amplified fragment length polymorphism analysis of Aspergillus carbonarius, Aspergillus tubingensis and Aspergillus niger strains isolated from grapes in Italy. Appl Environ Microbiol 72:680-685.
32. Peterson SW. 1995. Phylogenetic analysis of Aspergillus sections Cremei and Wentii, based on ribosomal DNA sequences. Mycol Res 99:1349-1355.
33. -. 2000. Phylogenetic relationships in Aspergillus based upon rDNA sequence analysis. In: Samson RA, Pitt JI, eds. Classification of Penicillium and Aspergillus: integration of modern taxonomic methods. Reading, UK: Harwood Publishers. p 323-356.
34. Pitt JI. 1980. The genus Penicillium and its teleomorphic states Eupenicillium and Talaromyces. New York: Academic Press.
35. Raper KB, Fennell DI. 1965. The genus Aspergillus. Baltimore: Williams & Wilkins Co.
36. Rieppel O. 2007. Species: kinds of individuals or individuals of a kind. Cladistics 23:373-384.
37. Rokas A, Carroll SB. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol 22: 1337-1344.
38. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
39. Samson RA. 1979. A compilation of the Aspergilli described since 1965. Stud Mycol 18:1-38.
40. -, Seifert KA, Kuijper AFA, Houbraken JAMP, Frisvad JC. 2004. Phylogenetic analysis of Penicillium subgenus Penicillium using partial β-tubulin sequences. Stud Mycol 49:175-200.
41. -, Houbraken JAMP, Kuijpers AFA, Frank JM, Frisvad JC. 2005. New ochratoxin A or sclerotium producing species in Aspergillus section Nigri. Stud Mycol 50:45- 61.
42. Serra R, Cabanes FJ, Perrone G, Castella G, Venancio A, Mule G, Kozakiewicz Z. 2006. Aspergillus ibericus: a new species of section Nigri isolated from grapes. Mycologia 98:295-306.
43. -, Peterson SW. 2007. Penicillium astrolabium and Penicillium neocrassum, two new species isolated from grapes and their phylogenetic placement in the P. olsonii and P. brevicompactum clade. Mycologia 99:78-87.
44. Sites JW, Marshall JC. 2003. Delimiting species: a renaissance issue in systematic biology. Trend Ecol Evol 18: 462-470.
45. Swofford DL. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunder-land, Massachusetts: Sinauer Associates.
46. Takada M, Horie Y, Abliz P. 2001. Two new heterothallic Neosartorya from African soil. Mycoscience 42:361-367.
47. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fung Genet Biol 31:21-32.
48. Thom C, Church MB. 1926. The Aspergilli. Baltimore: Williams & Wilkins Co.
49. -, Raper KB. 1945. Manual of the Aspergilli. Baltimore: Williams & Wilkins Co.
50. Thompson JD, Higgins DG, Gibson TJ. 1994. Clustal V: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 22:4673-4680.
51. Varga J, Tóth B, Kocsubó S, Farkas B, Szakács G, Téren J, Kozakiewicz Z. 2005. Evolutionary relationships among Aspergillus terreus isolates and their relatives. Antonie von Leeuwenhoek 88:141-150.
52. Wiley BJ, Simmons EG. 1973. New species and a new genus of Plectomycetes with Aspergillus states. Mycologia 65: 934-938.
53. -, Fennell DI. 1973. Ascocarps of Aspergillus stromatoides, A. niveus and A. flavipes. Mycologia 65:752-760.