Contamination, error, and nonspecific molecular tools

Random amplified polymorphic DNA (RAPD) and amplified fragment length polym orphism (AFLP) are widely used in studies of genetic variation. Although it is recognized that contamination should be avoided in DNA samples, little is known about the potential hazards of low level bacterial contamination o f samples from which DNA is extracted for RAPD or AFLP analyses. We found t hat contamination of Aphanomyces cochlioides cultures with a prokaryote at visibly undetectable levels markedly altered the results of RAPD and AFLP a nalyses. The contamination resulted in seven contaminant-specific RAPD prod ucts and in the suppression of eight products characteristic of uncontamina ted A. cochlioides cultures. Prokaryote contamination resulted in 39 contam inant-specific AFLP products, but did not cause suppression of AFLP product s. Comparing A. cochlioides samples with outgroup A. eutelches did not clea rly indicate the presence of contaminant DNA, because uneven product suppre ssion in RAPD analysis increased the apparent similarity between contaminat ed samples and A. eutelches and because a high proportion of the contaminan t-specific amplified products comigrated with products from A. euteiches in both RAPD and AFLP analyses. Work with organisms that are prone to contami nation should employ techniques such as restriction fragment length polymor phism or DNA sequence comparisons rather than relying solely on RAPD or AFL P analyses.