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Related Experiment Video

Updated: Jun 28, 2026

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

Published on: September 13, 2018

Contamination, error, and nonspecific molecular tools.

A T Dyer, K J Leonard

|October 24, 2008

Summary

Low-level bacterial contamination can significantly alter genetic analysis results. Even invisible prokaryote contamination in DNA samples can lead to inaccurate findings in Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) studies.

Area of Science:

Molecular Biology
Genetics
Microbiology

Background:

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) are common molecular markers for genetic variation.
The impact of low-level bacterial contamination on DNA extraction for RAPD and AFLP analyses is not well understood.

Purpose of the Study:

To investigate the effects of subtle prokaryote contamination on RAPD and AFLP analyses.
To assess the reliability of RAPD and AFLP in detecting contamination when comparing closely related species.

Main Methods:

DNA extraction from Aphanomyces cochlioides cultures.
Analysis of genetic variation using RAPD and AFLP techniques.
Comparison of contaminated and uncontaminated DNA samples, including outgroup comparison with Aphanomyces euteiches.

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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

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Cell Culture Techniques and Practices to Avoid Contamination by Fungi and Bacteria in the Research Cell Culture Laboratory

Cell Culture Techniques and Practices to Avoid Contamination by Fungi and Bacteria in the Research Cell Culture Laboratory

Published on: July 7, 2023

Main Results:

Bacterial contamination introduced specific RAPD products and suppressed native A. cochlioides products.
Prokaryote contamination generated numerous specific AFLP products but did not suppress existing ones.
Contamination masked true genetic differences, leading to apparent similarity between contaminated samples and the outgroup A. euteiches in both RAPD and AFLP.

Conclusions:

Visibly undetectable bacterial contamination can severely compromise the accuracy of RAPD and AFLP analyses.
RAPD and AFLP may not be reliable for detecting contamination in organisms prone to microbial presence.
Alternative methods like restriction fragment length polymorphism or DNA sequencing are recommended for contaminated samples.