Aspergillus and Penicillium identification using DNA sequences: Barcode or MLST?

Applied Microbiology and Biotechnology

Volumn 95, Issue 2, 2012, Pages 339-344

  Peterson, Stephen W ^a  

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

Author keywords

Barcode; MLST; Species concept; Trichocomaceae

Indexed keywords

DNA DATA; DNA TECHNOLOGY; IF THERE ARE; MLST; SINGLE NUCLEOTIDE POLYMORPHISMS; SINGLE NUCLEOTIDES; SPECIES CONCEPT; TAXONOMIC DIVERSITY; TRICHOCOMACEAE;

BAR CODES; DNA; GENES; NUCLEOTIDES;

ASPERGILLUS;

DNA; RIBOSOME RNA;

CLADISTICS; DATA SET; FUNGUS; GENETIC ANALYSIS; GENETIC MARKER; IDENTIFICATION METHOD; MOLECULAR ANALYSIS; SPECIES CONCEPT; TAXONOMY;

ASPERGILLUS; BARCODE; BIOTECHNOLOGICAL PROCEDURES; DNA SEQUENCE; FUNGUS; GENOTYPE; MULTILOCUS SEQUENCE TYPING; NOMENCLATURE; NONHUMAN; PENICILLIUM; PHENOTYPE; PHYLOGENY; REVIEW; SPECIES; TAXONOMY; TRICHOCOMACEAE;

ASPERGILLUS; DNA BARCODING, TAXONOMIC; DNA, FUNGAL; MULTILOCUS SEQUENCE TYPING; PENICILLIUM;

ASPERGILLUS; PENICILLIUM; TRICHOCOMACEAE;

EID: 84864687992     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4165-2     Document Type: Review

References (51)

1. Anderson B, Frisvad JC, Sondergaard I, Rasmussen IB, Larsen LS (2011) Associations between fungal species and water-damaged building materials. Appl Environ Microbiol 77:4180-4188
2. Balajee SA (2008) DNA based methods for species identification in the genus Aspergillus. In: Varga J, Samson RA (eds) Aspergillus in the genomic era. Wageningen Academic, Wageningen, pp 261-276
3. Balmas V, Migheli Q, Scherm B, Garau P, O'Donnell K, Ceccherelli G, Kang S, Geiser DM (2010) Multilocus phylogenetics show high levels of endemic fusaria inhabiting Sardinian soils (Tyrrhenian Islands). Mycologia 102:803-812
4. Benjamin CR (1955) Ascocarps of Aspergillus and Penicillium. Mycologia 47:669-687
5. De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879-886 (Pubitemid 350129638)
6. Dettman JR, Jacobson DJ, Turner E, Pringle A, Taylor JW (2003) Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model Eukaryote. Evolution 57:2721-2741 (Pubitemid 38078354)
7. Dettman JR, Jacobson DJ, Taylor JW (2006) Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex. Mycologia 98:436-446 (Pubitemid 44440919)
8. Dhillon GS, Brar SK, Kaur S, Verma M (2012) Rheological studies during submerged citric acid fermentation by Aspergillus niger in stirred fermentors using apple pomace ultrafiltration sludge. Food Bioprocess Technol. doi:10.1007/s11947-011-0771-8
9. Doolittle WF, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci (USA) 104:2043-2049 (Pubitemid 46391349)
10. Dupont J, Dutertre M, Lafay J-F, Roquebert MF, Brygoo Y (1990) A molecular assessment of the position of Stilbothamnium in the genus Aspergillus. In: Samson RA, Pitt JI (eds) Modern concepts in Penicillium and Aspergillus classification. Plenum, New York, pp 335-342
11. Eberhardt U (2010) A constructive step towards selecting a DNA barcode for fungi. New Phytol 187:266-268
12. Edman JC, Kovacs JA, Masur H, Santi DV, Elwood HJ, Sogin ML (1986) Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature 334:519-522
13. Ereshefsky M (2011) Mystery of mysteries: Darwin and the species problem. Cladistics 27:67-79
14. Frisvad JC, Filtenborg O (1989) Terverticillate penicillia: chemotaxonomy and mycotoxin production. Mycologia 81:837-861
15. 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
16. Horn BW, Moore GG, Carbone I (2009) Sexual reproduction in Aspergillus flavus. Mycologia 101:423-429
17. Houbraken J, Due M, Varga J, Meijer M, Frisvad JC, Samson RA (2007) Polyphasic taxonomy of Aspergillus section Usti. Stud Mycol 59:107-128 (Pubitemid 351155592)
18. Houbraken J, López-Quintero CA, Frisvad JC, Boekhout T, Theelen B, Franco-Molano AE, Samson RA (2011) Penicillium araracuarense sp. nov., Penicillium elleniae sp. nov., Penicillium penarojense sp. nov., Penicillium vanderhammenii sp. nov. and Penicillium wotroi sp. nov., isolated from leaf litter. Int J Syst Evol Microbiol 61:1462-1475
19. Knapp S, McNeil J, Turland NJ (2011) Fungal Nomenclature. Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? Mycotaxon 117:509-515
20. Kozakiewicz Z (1989) Aspergillus species on stored products. Mycol Pap 161:1-188
21. Logrieco A, Peterson SW, Wicklow DT (1990) Ribosomal RNA comparisons among taxa of the terverticillate penicillia. In: Samson RA, Pitt JI (eds) Modern concepts in Penicillium and Aspergillus classification. Plenum, New York, pp 343-356
22. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci (USA) 95:3140-3145 (Pubitemid 28135868)
23. McNeil J, Turland NJ (2011) Major changes to the Code of Nomenclature - Melbourne, July 2011. Taxon 60:1495-1497
24. Norvell LL (2011) Melbourne approves a new CODE. Mycotaxon 116:481-490
25. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337-365
26. Perrone G, Stea G, Epifani F, Varga J, Frisvad JC, Samson RA (2011) Aspergillus niger contains the cryptic phylogenetic species A. awamori. Fungal Biol 115:1138-1150
27. Peterson SW (1992) Neosartorya pseudofischeri sp. nov. and its relationship to other species in Aspergillus section Fumigati. Mycol Res 96:547-554
28. Peterson SW (2000) Phylogenetic analysis of Penicillium based on ITS and LSU-rDNA sequences. In: Samson RA, Pitt JI (eds) Classification of Penicillium and Aspergillus: integration of modern taxonomic methods. Harwood, Reading, pp 163-178
29. Peterson SW (2008) Phylogenetic analysis of Aspergillus species using DNA sequences from four loci. Mycologia 100:191-212
30. Peterson SW, Horn BW (2009) Penicillium parvulum and Penicillium georgiense, sp. nov. isolated from the conidial heads of Aspergillus species. Mycologia 101:71-83
31. Peterson SW, Orchard SS, Menon S (2011) Penicillium menonorum, a new species related to P. pimiteouiense. IMA Fungus 2:121-125
32. Pitt JI, Samson RA, Frisvad JC (2000) List of accepted species and their synonyms in the family Trichocomaceae. In: Samson RA, Pitt JI (eds) Integration of modern taxonomic methods for Penicillium and Aspergillus classification. Harwood Academic, Amsterdam, pp 9-50
33. Raper KB, Fennell DI (1965) The genus Aspergillus. Williams and Wilkins, Baltimore
34. Raper KB, Thom C (1949) A manual of the penicillia. Williams and Wilkins, Baltimore
35. Samson RA, Frisvad JC (2004) Penicillium subgenus Penicillium: new taxonomic schemes, mycotoxins and other extrolites. Stud Mycol 49:1-260
36. Samson RA, Yilmaz N, Houbraken J, Spierenburg H, Seifert KA, Peterson SW, Varga J, Frisvad JC (2011) Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium. Stud Mycol 70:159-184
37. Sant'Ana AS, Simas RC, Almeida CAA, Cabral EC, Rauber RH, Mallmann CA, Everlin MN, Resenthal A, Massaguer PR (2010) Influence of package, type of apple juice and temperature on the production of patulin by Byssochlamys nivea and Byssochlamys fulva. Int J Food Microbiol 142:156-163
38. Schoch CL, Seifert KA, Huhndorf S, Robert V, Souge JL, Levesque CA, Chen W, Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci (USA) doi: 10.1073/pnas.1117018109; Available at: www.pnas.org/cgi/doi/10. 1073/pnas.1117018109
39. Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9(suppl 1):83-89
40. Seifert KA, Samson RA, deWaard JR, Houbraken J, Lévesque CA, Moncalvo J-M, Louis-Seize G, Hebert PDN (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci (USA) 104:3901-3906 (Pubitemid 47181551)
41. Short DPG, O'Donnell K, Zang N, Juba JH, Geiser DM (2011) Widespread occurrence of diverse human pathogenic types of the fungus Fusarium detected in plumbing drains. J Clin Microbiol 49:4264-4272
42. Simpson GG (1951) The species concept. Evolution 5:285-298
43. Soares C, Rodrigues P, Peterson SW, Lima N, Venâncio A (2012) Three new species of Aspergillus section Flavi isolated from almonds and maize in Portugal. Mycologia. doi:10.3852/11-088
44. Stolk AC, de Scott B (1967) Studies on the genus Eupenicillium Ludwig. I. Taxonomy and nomenclature of Penicillia in relation to their sclerotioid ascocarpic states. Persoonia 4:391-405
45. Stolk AC, Samson RA (1971) Studies on Talaromyces and related genera I. Hamigera gen. nov. and Byssochlamys. Persoonia 6:341-357
46. Sudjaritruk T, Sirisanthana T, Sirisanthana V (2012) Immune reconstitution inflammatory syndrome from Penicillium marneffei in an HIV-infected child: a case report and review of literature. BMC Infect Dis 12:28
47. 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 31:21-32 (Pubitemid 32066164)
48. Varga J, Frisvad JC, Kocsubé S, Bankovics B, Tóth B, Szigeti G, Samson RA (2011) New and revisited species in Aspergillus section Nigri. Stud Mycol 69:1-17
49. Veršilovskis A, Saeger SD (2010) Sterigmatocystin: occurrence in foodstuffs and analytical methods - an overview. Mol Nutr Food Res 54:136-147
50. Walsh TJ, Wissel MC, Grantham KJ, Petraitiene R, Petraitis V, Kasai M, Francesconi A, Cotton MP, Hughes JE, Greene L, Bacher JD, Manna P, Salomoni M, Kleiboeker SB, Reddy SK (2011) Molecular detection and species-specific identification of medically important Aspergillus species by real-time PCR in experimental invasive pulmonary aspergillosis. J Clin Microbiol 49:4150-4157
51. Xu X, Yang J, An Y, Pan Y, Liu G (2012) Over-expression of pcvA involved in vesicle-vacuolar fusion affects the conidiation and penicillin production in Penicillium chrysogenum. Biotechnol Lett 34:519-526