Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP

Holger Schmidt; Matthias Ehrmann; Rudi F. Vogel; Marta H. Taniwaki; Ludwig Niessen

doi:10.1078/072320203322337434

Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP

Holger Schmidt, Matthias Ehrmann, Rudi F. Vogel, Marta H. Taniwaki, Ludwig Niessen

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Abstract

70 strains of Aspergillus ochraceus mainly isolated from Brazilian coffee related sources were investigated for genetic relatedness using automated laser fluorescence analysis of AFLP fragments. Cluster analysis of fingerprints revealed a very close relationship among most of the strains. Based on these results, a sub-set of characteristic A. ochraceus strains was chosen for the detection of marker sequences. These sequences were obtained from silver stained AFLPs separated on polyacrylamide gels. A number of bands characteristic for A. ochraceus were detected and cut out from the gels. DNA was reamplified, cloned and fragments were sequenced. Based on these sequences a set of SCAR PCR-primers was constructed. PCRs were optimised for specificity and subsequently tested against a panel of Aspergillus species. Using this approach a PCR specific for Aspergillus ochraceus was developed.

Original language	English
Pages (from-to)	138-146
Number of pages	9
Journal	Systematic and Applied Microbiology
Volume	26
Issue number	1
DOIs	https://doi.org/10.1078/072320203322337434
State	Published - Mar 2003

Keywords

AFLP
Aspergillus ochraceus
Coffee
Detection
PCR
SCAR
Taxonomy

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10.1078/072320203322337434

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@article{36e7cec6b3564d11a7be91b81dbe3507,

title = "Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP",

abstract = "70 strains of Aspergillus ochraceus mainly isolated from Brazilian coffee related sources were investigated for genetic relatedness using automated laser fluorescence analysis of AFLP fragments. Cluster analysis of fingerprints revealed a very close relationship among most of the strains. Based on these results, a sub-set of characteristic A. ochraceus strains was chosen for the detection of marker sequences. These sequences were obtained from silver stained AFLPs separated on polyacrylamide gels. A number of bands characteristic for A. ochraceus were detected and cut out from the gels. DNA was reamplified, cloned and fragments were sequenced. Based on these sequences a set of SCAR PCR-primers was constructed. PCRs were optimised for specificity and subsequently tested against a panel of Aspergillus species. Using this approach a PCR specific for Aspergillus ochraceus was developed.",

keywords = "AFLP, Aspergillus ochraceus, Coffee, Detection, PCR, SCAR, Taxonomy",

author = "Holger Schmidt and Matthias Ehrmann and Vogel, {Rudi F.} and Taniwaki, {Marta H.} and Ludwig Niessen",

note = "Funding Information: We wish to thank C. Seeliger and M. Bannier for technical assistance and Maher Korakli for critical reviewing of the manuscript. This work was supported by the EU Project DeTox-Fungi (European Commission, Quality of Life and Management of Living Resources Programme (QOL), Key Action 1 on Food, Nutrition and Health, Contract No. QLK1-CT-1999-01380).",

year = "2003",

month = mar,

doi = "10.1078/072320203322337434",

language = "English",

volume = "26",

pages = "138--146",

journal = "Systematic and Applied Microbiology",

issn = "0723-2020",

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TY - JOUR

T1 - Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP

AU - Schmidt, Holger

AU - Ehrmann, Matthias

AU - Vogel, Rudi F.

AU - Taniwaki, Marta H.

AU - Niessen, Ludwig

N1 - Funding Information: We wish to thank C. Seeliger and M. Bannier for technical assistance and Maher Korakli for critical reviewing of the manuscript. This work was supported by the EU Project DeTox-Fungi (European Commission, Quality of Life and Management of Living Resources Programme (QOL), Key Action 1 on Food, Nutrition and Health, Contract No. QLK1-CT-1999-01380).

PY - 2003/3

Y1 - 2003/3

N2 - 70 strains of Aspergillus ochraceus mainly isolated from Brazilian coffee related sources were investigated for genetic relatedness using automated laser fluorescence analysis of AFLP fragments. Cluster analysis of fingerprints revealed a very close relationship among most of the strains. Based on these results, a sub-set of characteristic A. ochraceus strains was chosen for the detection of marker sequences. These sequences were obtained from silver stained AFLPs separated on polyacrylamide gels. A number of bands characteristic for A. ochraceus were detected and cut out from the gels. DNA was reamplified, cloned and fragments were sequenced. Based on these sequences a set of SCAR PCR-primers was constructed. PCRs were optimised for specificity and subsequently tested against a panel of Aspergillus species. Using this approach a PCR specific for Aspergillus ochraceus was developed.

AB - 70 strains of Aspergillus ochraceus mainly isolated from Brazilian coffee related sources were investigated for genetic relatedness using automated laser fluorescence analysis of AFLP fragments. Cluster analysis of fingerprints revealed a very close relationship among most of the strains. Based on these results, a sub-set of characteristic A. ochraceus strains was chosen for the detection of marker sequences. These sequences were obtained from silver stained AFLPs separated on polyacrylamide gels. A number of bands characteristic for A. ochraceus were detected and cut out from the gels. DNA was reamplified, cloned and fragments were sequenced. Based on these sequences a set of SCAR PCR-primers was constructed. PCRs were optimised for specificity and subsequently tested against a panel of Aspergillus species. Using this approach a PCR specific for Aspergillus ochraceus was developed.

KW - AFLP

KW - Aspergillus ochraceus

KW - Coffee

KW - Detection

KW - PCR

KW - SCAR

KW - Taxonomy

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U2 - 10.1078/072320203322337434

DO - 10.1078/072320203322337434

M3 - Article

C2 - 12747422

AN - SCOPUS:0037368731

SN - 0723-2020

VL - 26

SP - 138

EP - 146

JO - Systematic and Applied Microbiology

JF - Systematic and Applied Microbiology

IS - 1

ER -

Molecular typing of Aspergillus ochraceus and construction of species specific SCAR-primers based on AFLP

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Keywords

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