Primer set details

ORGANISM
Complete name : Fusarium tricinctum
Database ID : 575
INTERNET RESOURCES
Google Wikispecies, the free species directory Wikipedia, The Free Encyclopeda
NCBI Taxonomy Browser CABI Index Fungorum CBS Anamorph/Teleomorph

PRIMER SET (5’→3′)
Forward Primer Select to Blast
Name : FtricACL1-f Sequence :
Reverse Primer
Name : FtricACL1-r Sequence :
TARGET DNA (Amplicon size)
ATP citrate lyase gene (425 bp)
PCR TECHNIQUE
Conventional PCR
REMARKS
The paper reports other primer pairs for an alternative PCR based detection technology, the loop-mediated isothermal amplification (LAMP) of DNA. The current database architecture does not support LAMP primers, so users are asked to check the original paper for primer sequences and details.
REFERENCE
Authors : Niessen L., Gräfenhan T., Vogel R.F.
Year : 2012
Title : ATP citrate lyase 1 (acl1) gene-based loop-mediated amplification assay for the detection of the Fusarium tricinctum species complex in pure cultures and in cereal samples
Journal : International Journal of Food Microbiology
Volume : 158
Pages : 171-185
DOI: 10.1016/j.ijfoodmicro.2012.06.021
Abstract : The combined data set of the acl1 and tef-1a gene sequences of 61 fungal strains assigned to Fusarium tricinctum, Fusarium avenaceum, Fusarium acuminatum, Fusarium arthrosporioides, Fusarium flocciferum and Fusarium torulosum were used to study the phylogenetic relations between taxa. F. tricinctum, F. acuminatum and F. avenaceum formed distinct clades. Members of the F. tricinctum/F. acuminatum clade fall into three well supported lineages, of which the largest includes the epitype of F. tricinctum. Loop-mediated isothermal amplification (LAMP) was used to amplify a 167 bp portion of the acl1 gene in F. tricinctum (Corda) Saccardo. DNA amplification was detected in-tube by indirect calcein fluorescence under black light after 60 min of incubation at 65.5 °C. The assay had a detection limit of 0.95 pg of purified genomic DNA of F. tricinctum CBS 410.86 per reaction, corresponding to ca. 18 genomic copies of the acl1 gene. Specificity of the assay was tested using purified DNA from 67 species and subspecies of Fusarium as well as 50 species comprising 22 genera of other filamentous fungi and yeasts. The assay detected 21 of the 23 F. tricinctum strains tested. Cross reactivity was observed with eight out of 13 strains in F. acuminatum but with none of 17 F. avenaceum strains tested. Specificity was further confirmed by conventional PCR with primers designed from the same gene. Detection of F. tricinctum from culture scrapings directly added to the reaction master mix, in DNA extracts from wheat, in single barley grains or in washings of bulk grain samples are proposed as possible applications showing the suitability of the method for food analysis. Finally it was demonstrated that the LAMP reaction can be run using simple lab equipment such as a heating block, water bath, hybridization oven or household equipment, e.g. a microwave oven.
SUBMITTER
Dr. Quirico Migheli
qmigheli@uniss.it
University of Sassari
Department of Agricultural Sciences, Plant Pathology and Entomology Unit
Via E. De Nicola 9, I-07100 Sassari
Italy
Record creation : 2012-08-31 Last record update : 2012-08-31

* Disclaimer *

No guarantee can be given for the correctness of the data presented.
Although the DNA sequences were reviewed for accuracy,
original pubblications should be consulted to verify their composition.

Back