Comparison of AFLP and rep-PCR genomic fingerprinting with DNA--DNA homology studies: Xanthomonas as a model system

This study compared two rapid PCR-based genomic fingerprinting techniques—rep-PCR and AFLP—with DNA-DNA hybridization, which is the gold standard for bacterial species definition. The researchers analyzed 178 Xanthomonas strains representing all 20 previously identified DNA-DNA homology groups, plus a Stenotrophomonas maltophilia control strain. Rep-PCR fingerprints were generated using three primer sets (BOX, ERIC, REP), while AFLP fingerprints were produced from 80 of these strains. Computer-assisted analysis calculated similarity values from fingerprint patterns and compared them to DNA-DNA homology values. The results showed high statistically significant correlations between rep-PCR similarity values and DNA-DNA homology (r=0.779 for combined BOX-ERIC-REP) and between AFLP and DNA-DNA homology (r=0.838). Cluster analysis dendrograms from both fingerprinting methods corresponded precisely to DNA-DNA homology groupings, with only minor exceptions in the highly heterogeneous Group 9 (Xanthomonas axonopodis). These findings validate genomic fingerprinting as a rapid, practical alternative to DNA-DNA hybridization for bacterial taxonomic classification and diversity assessment.

Key findings

• Rep-PCR and AFLP fingerprinting showed high positive correlations with DNA-DNA homology values (r=0.779-0.838), demonstrating their validity for bacterial species classification
• Cluster analysis dendrograms from both fingerprinting techniques corresponded precisely to the 20 DNA-DNA homology groups identified in Xanthomonas species
• Combined rep-PCR patterns (BOX-ERIC-REP) produced higher correlation values than individual methods, suggesting that multiple repetitive element types provide better phylogenetic resolution
• Genomic fingerprinting techniques enable rapid, high-resolution screening for bacterial taxonomic diversity and phylogenetic relationships without the time-consuming pair-wise DNA-DNA hybridization analysis