Primer set details

ORGANISM
Complete name : Colletotrichum spp.
Database ID : 334
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 : Cc1F1 Sequence :
Reverse Primer
Name : Cc2R1 Sequence :
TARGET DNA (Amplicon size)
ITS region (447 bp)
PCR TECHNIQUE
Conventional PCR
REFERENCE
Authors : Cullen D.W., Lees A.K., Toth I.K., Duncan J.M.
Year : 2002
Title : Detection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR
Journal : Plant Pathology
Volume : 51
Pages : 281-292
Abstract : Colletotrichum coccodes is the causal agent of the potato blemish disease black dot. Two PCR primer sets were designed to sequences of the ribosomal internal transcribed spacer (ITS1 and ITS2) regions for use in a nested PCR. The genus-specific outer primers (Cc1F1/Cc2R1) were designed to regions common to Colletotrichum spp., and the species-specific nested primers (Cc1NF1/Cc2NR1) were designed to sequences unique to C. coccodes. The primer sets amplified single products of 447 bp (Cc1F1/Cc2R1) and 349 bp (Cc1NF1/Cc2NR1) with DNA extracted from 33 European and North American isolates of C. coccodes. The specificity of primers Cc1NF1/Cc2NR1 was confirmed by the absence of amplified product with DNA of other species representing the six phylogenetic groups of the genus Colletotrichum and 46 other eukaryotic and prokaryotic plant pathogenic species. A rapid procedure for the direct extraction of DNA from soil and potato tubers was used to verify the PCR assay for detecting C. coccodes in environmental samples. The limit of sensitivity of PCR for the specific detection of C. coccodes when inoculum was added to soils was 3.0 spores per g, or the equivalent of 0.06 microsclerotia per g soil, the lowest level of inoculum tested. Colletotrichum coccodes was also detected by PCR in naturally infested soil and from both potato peel and peel extract from infected and apparently healthy tubers. Specific primers and a TaqMan fluorogenic probe were designed to perform quantitative real-time (TaqMan) PCR to obtain the same levels of sensitivity for detection of C. coccodes in soil and tubers during a first-round PCR as with conventional nested PCR and gel electrophoresis. This rapid and quantitative PCR diagnostic assay allows an accurate estimation of tuber and soil contamination by C. coccodes.
SUBMITTER
Dr. Stefano Ghignone (Sistem Administrator)
stefano.ghignone@ipsp.cnr.it
Consiglio Nazionale delle Ricerche (CNR)
Istituto per la Protezione delle Piante, Sez. Torino
V.le P.A. Mattioli 25, I-10125 Turin
Italy
Record creation : 2004-09-25 Last record update : 2004-09-25

* 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.

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