Characterization of penicillium species by ribosomal DNA sequencing and BOX, ERIC and REP-PCR analysis

Mycopathologia

Volumn 168, Issue 1, 2009, Pages 11-22

  Redondo, Cristina ^a   Cubero, Jaime ^a   Melgarejo, Paloma ^a  

^a INIA   (Spain)

Author keywords

Biocontrol; DNA fingerprinting; Fungal monitoring; Internal transcribed spacers; Rep PCR

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

ARTICLE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA SEQUENCE; GENETICS; GENOTYPE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PENICILLIUM; PHYLOGENY;

CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; GENOTYPE; MOLECULAR SEQUENCE DATA; PENICILLIUM; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ENTEROBACTERIACEAE; PENICILLIUM; PENICILLIUM GLABRUM; PENICILLIUM OXALICUM; PENICILLIUM PURPUROGENUM;

EID: 67650600605     PISSN: 0301486X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11046-009-9191-y     Document Type: Article

References (59)

1. Thom C. The Penicillia. London: Baillière Tindall and Cox; 1930.
2. Raper KB, Thom C. A manual of the Penicillia. Baltimore, USA: Williams & Wilkins Co.; 1949.
3. KA Seifert CA Levesque 2004 Phylogeny and molecular diagnosis of mycotoxigenic fungi Eur J Plant Pathol 110 449 471 10.1023/B:EJPP.0000032385. 41877.7a
4. Pitt JI. The genus Penicillium and its teleomorphic states Eupenicillium and Talaromyces. London: Academic Press; 1979.
5. Ramirez C. Manual and atlas of the Penicillia. Amsterdam, The Netherlands: Elsevier Biomedical Press; 1982.
6. W Meyer A Koch C Niemann B Beyermann JT Epplen T Borner 1991 Differentiation of species and strains among filamentous fungi by DNA fingerprinting Curr Gen 19 239 242 10.1007/BF00336493
7. AHS Onions PD Bridge RR Paterson 1984 Problems and prospects for the taxonomy of Penicillium Microbiol Sci 1 185 189 (Pubitemid 16254144)
8. JC Frisvad RA Samson 2004 Polyphasic taxonomy of Penicillium subgenus Penicillium. A guide to identification of food and air-borne terverticillate Penicillia and their mycotoxins Stud Mycol 49 1 173 10.1016/S0922-5382(04)80002- 3 (Pubitemid 39648989)
9. J Smedsgaard J Nielsen 2005 Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics J Exp Bot 56 273 286 10.1093/jxb/eri068
10. MJ Pianzzola M Moscatelli S Vero 2004 Characterization of Penicillium isolates associated with blue mold on apple in Uruguay Plant Dis 88 23 28 10.1094/PDIS.2004.88.1.23 (Pubitemid 38390463)
11. RRM Paterson A Venancio N Lima 2004 Solutions to Penicillium taxonomy crucial to mycotoxin research and health Res Microbiol 155 507 513 10.1016/j.resmic.2004.04.001
12. RH Cruickshank JI Pitt 1987 Identification of species in Penicillium Subgenus Penicillium by enzyme electrophoresis Mycologia 79 614 620 10.2307/3807602
13. F Fierro JL Barredo B Diez S Gutierrez FJ Fernandez FJ Martin 1995 The Penicillin gene cluster is amplified in tandem repeats linked by conserved hexanucleotide sequences Proc Nat Acad Sci USA 92 6200 6204 10.1073/pnas.92.13. 6200
14. J Dupont S Magnin A Marti M Brousse 1999 Molecular tools for identification of Penicillium starter cultures used in the food industry Int J Food Microbiol 49 109 118 10.1016/S0168-1605(99)00055-0
15. RA Samson KA Seifert AFA Kuijpers JAMP Houbraken JC Frisvad 2004 Phylogentic analysis of Penicillium subgenus Penicillium using partial β-tubulin sequences Stud Mycol 49 175 200 (Pubitemid 39648990)
16. S La Guerche C Garcia P Darriet D Dubourdieu J Labarere 2004 Characterization of Penicillium species isolated from grape berries by their internal transcribed spacer (ITS1) sequences and by gas chromatography-mass spectrometry analysis of geosmin production Curr Microbiol 48 405 411 (Pubitemid 38656897)
17. KA Seifert RA Samson JR de Waard J Houbraken CA Levesque JM Moncalvo G Louis-Seize PDN Hebert 2007 Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as test case Proc Nat Acad Sci USA 104 3901 3906 10.1073/pnas.0611691104
18. SW Peterson L Sigler 2002 Four new Penicillium species having Thysanophora-like melanized conidiophores Mycol Res 106 1109 1118 10.1017/S0953756202006433
19. SW Peterson J Perez FE Vega F Infante 2003 Penicillium brocae, a new species associated with the coffee berry borer in Chiapas, Mexico Mycologia 95 141 147 10.2307/3761973 (Pubitemid 36247214)
20. Peterson SW. Phylogenetic analysis of Penicillium species based on ITS and lsu-rDNA nucleotide differences. In: Samson RA, Pitt JI, editors. Integration of modern taxonomic methods for Penicillium and Aspergillus classification. Amsterdam: Harwood Academic Publishers; 2000. p. 163-78.
21. SW Peterson 2004 Multilocus DNA sequence analysis shows that Penicillium biourgeianum is a distinct species closely related to P. brevicompactum, P. olsonii Mycol Res 108 434 440 10.1017/S0953756204009761
22. P Skouboe JC Frisvad JW Taylor D Lauritsen M Boysen L Rossen 1999 Phylogenetic analysis of nucleotide sequences from the ITS region of terverticillate Penicillium species Mycol Res 103 873 881 10.1017/ S0953756298007904
23. J Scott WA Untereiner B Wong NA Straus D Malloch 2004 Genotypic variation in Penicillium chrysogenum from indoor environments Mycologia 96 1095 1105 10.2307/3762092 (Pubitemid 39415027)
24. DE Tuthill 2004 Genetic variation and recombination in Penicillium miczynskii and Eupenicillium, species Mycol Prog 3 3 12 10.1007/s11557-006-0070- 3
25. CSJ Hulton CF Higgins PM Sharp 1991 ERIC sequences-a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria Mol Microbiol 5 825 834 10.1111/j.1365-2958.1991. tb00755.x (Pubitemid 21896105)
26. M Gillings M Holley 1997 Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements Lett Appl Microbiol 25 17 21 10.1046/j.1472-765X.1997.00162.x (Pubitemid 27306044)
27. V Edel C Steinberg I Avelange G Laguerre C Alabouvette 1995 Comparison of 3 molecular methods for the characterization of Fusarium oxysporum strains Phytopathology 85 579 585 10.1094/Phyto-85-579
28. MCC de Arruda RNG Millar MASV Ferreira MSS Felipe 2003 Comparison of Crinipellis perniciosa isolates from Brazil by ERIC repetitive element sequence-based PCR genomic fingerprinting Plant Pathol 52 236 244 10.1046/j.1365-3059.2003.00819.x
29. FJ Reynaldi AC Lopez GN Albo AM Alippi 2003 Differentiation of Ascosphaera apis isolates by rep-PCR fingerprinting and determination of chalkbrood incidence in Argentinean honey samples J Apic Res 42 68 76 (Pubitemid 38075017)
30. G Berg C Zachow J Lottmann M Gotz R Costa K Smalla 2005 Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae Kleb Appl Environ Microb 71 4203 4213 10.1128/AEM.71.8.4203-4213.2005
31. JC Frisvad F Lund S Elmholt 2005 Ochratoxin A producing Penicillium verrucosum isolates from cereals reveal large AFLP fingerprinting variability J Appl Microbiol 98 684 692 10.1111/j.1365-2672.2004.02509.x
32. C Oliveri A Campisano C Catera G Cirvilleri 2007 Characterization and fAFLP genotyping of Penicillium strains from postharvest samples and packinghouse environments J Plant Pathol 89 29 40 (Pubitemid 46625665)
33. Goettel M S, Hajek AE, Siegel JP, Evans HC. Safety of fungal biocontrol agents. In: Butt TM, Jackson CW, Magan N, editors. Fungi as biological control agents: progress, problems and potential, CABI Publishing: Oxon; 2001. p. 347-375.
34. Council Directive 2005/25/EC of 14 March 2005 amending Annex VI to Directive 91/414/EEC as regards plant protection products containing micro-organisms. Official J Eur Union L 90, 2005;48(8):1-34.
35. A De Cal E M-Sagasta P Melgarejo 1990 Biological control of peach twig blight (Monilinia laxa) with Penicillium frequentans Plant Pathol 39 612 618 10.1111/j.1365-3059.1990.tb02542.x
36. I Larena P Melgarejo 1996 Biological control of plant pathogens by a lytic-enzyme-producing Penicillium purpurogenum Biol Control 6 631 637 10.1006/bcon.1996.0046
37. P Sabuquillo A De Cal P Melgarejo 2006 Biocontrol of tomato wilt by Penicillium oxalicum formulations in different crop conditions Biol Control 37 256 265 10.1016/j.biocontrol.2006.02.009
38. Bidochka MJ. Monitoring the fate of biocontrol fungi. In: Butt TM, Jackson CW, Magan N, editors. Fungi as biological control agents: progress, problems and potential. Oxon: CABI Publising; 2001. p. 193-218.
39. P Melgarejo R Carrillo E M-Sagasta 1985 Mycoflora of peach twigs and lowers and its possible significance in biological control of Monilinia laxa Trans Brit Mycol Soc 85 313 317
40. A De Cal S Pascual P Melgarejo 1997 Involvement of resistance induction by Penicillum oxalicum in the biocontrol of tomato wilt Plant Pathol 46 72 79 10.1046/j.1365-3059.1997.d01-204.x
41. J Keijer PM Houterman AM Dullemans MG Korsman 1996 Heterogeneity in electrophoretic karyotype within and between anastomosis groups of Rhizoctonia solani Mycol Res 100 789 797 (Pubitemid 26389823)
42. Sambrook J, Russsell DW. Molecular cloning: a laboratory manual. New York: Cold Spring Harbor; 2001.
43. White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR protocols: a guide to methods and applications. San Diego: Academic Press; 1990. p. 315-22.
44. TA Hall 1999 Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/Nt Nucleic Acids Symp Ser 41 95 98
45. JD Thompson DG Higgins TJ Gibson 1994 Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680 10.1093/nar/22.22.4673 (Pubitemid 24354800)
46. S Kumar K Tamura IB Jakobse M Nei 2001 Mega2: molecular evolutionary genetic analysis software Bioinformatics 17 1244 1245 10.1093/bioinformatics/17. 12.1244 (Pubitemid 33735359)
47. N Saitou M Nei 1987 The neighbor-joining method-a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
48. Jukes TH, Cantor RC. Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press; 1969. p. 21-132.
49. FJ Louws JLW Rademaker FJ de Bruijn 1999 The three Ds of PCR-based genomic analysis of phytobacteria: diversity, detection, and disease diagnosis Ann Rev Phytopathol 37 81 125 10.1146/annurev.phyto.37.1.81
50. LR Dice 1945 Measures of the amount of ecological association between species Ecology 26 297 302 10.2307/1932409
51. LPNM Kroon ECP Verstappen LFF Kox WG Flier PJM Bonants 2004 A rapid diagnostic test to distinguish between American and European populations of Phytophthora ramorum Phytopathology 94 613 620 10.1094/PHYTO.2004.94.6.613 (Pubitemid 38681970)
52. DR Soll 2000 The ins and outs of DNA fingerprinting the infectious fungi Clin Microbiol Rev 13 332 369 10.1128/CMR.13.2.332-370.2000
53. I Alvarez JF Wendel 2003 Ribosomal ITS sequences and plant phylogenetic inference Mol Phylogenet Evol 29 417 434 10.1016/S1055-7903(03)00208-2
54. RA Haugland JL Heckman LJ Wymer 1999 Evaluation of different methods for the extraction of DNA from fungal conidia by quantitative competitive PCR analysis J Microbiol Meth 37 165 176 10.1016/S0167-7012(99)00061-5
55. L Turin F Riva G Galbiati T Cainelli 2000 Fast, simple and highly sensitive double-rounded polymerase chain reaction assay to detect medically relevant fungi in dermatological specimens Eur J Clin Invest 30 511 518 10.1046/j.1365-2362.2000.00659.x
56. ML Berbee A Yoshimura J Sugiyama JW Taylor 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 10.2307/3760907
57. T Yua L Wangb Y Yina Y Wanga X Zhenga 2008 Effect of chitin on the antagonistic activity of Cryptococcus laurentii against Penicillium expansum in pear fruit Int J Food Microbiol 122 44 48 10.1016/j.ijfoodmicro.2007.11.059
58. J Cubero JH Graham 2002 Genetic relationship among worldwide strains of Xanthomonas causing canker in citrus species and design of new primers for their identification by PCR Appl Environ Microb 68 1257 1264 10.1128/AEM.68.3.1257- 1264.2002
59. MG Milgroom TL Peever 2003 Population biology of plant pathogens-the synthesis of plant disease epidemiology and population genetics Plant Dis 87 608 617