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

Abstract

The genus Xanthomonas contains a large number of strains, which have been characterized by a variety of phenotypic and genotypic classification methods. The Xanthomonas collection constitutes one of the largest groups of bacteria that have been characterized phylogenetically by DNA-DNA homology studies and genomic fingerprinting. Presently, a total genomic DNA-DNA homology value of 70 % represents an internationally accepted criterion to define bacterial species levels. However, the complexity of DNA-DNA reassociation kinetics methods precludes the rapid analysis of large numbers of bacterial isolates, which is imperative for molecular microbial diversity studies. Therefore, the aim of this study was to compare more facile PCR-based genomic fingerprinting techniques, such as repetitive-sequence-based (rep)-PCR and AFLP genomic fingerprinting, to DNA-DNA hybridization studies. Using three different primer sets, rep-PCR genomic fingerprint patterns were generated for 178 Xanthomonas strains, belonging to all 20 previously defined DNA-DNA homology groups, and one Stenotrophomonas maltophilia strain. In addition, AFLP genomic fingerprints were produced for a subset of 80 Xanthomonas strains belonging to the 20 DNA-DNA homology groups and for the S. maltophilia strain. Similarity values derived from rep-PCR-and AFLPgenerated fingerprinting analyses were calculated and used to determine the correlation between rep-PCR-or AFLP-derived relationships and DNA-DNA homology values. A high correlation was observed, suggesting that genomic fingerprinting techniques truly reveal genotypic and phylogenetic relationships of organisms. On the basis of these studies, we propose that genomic fingerprinting techniques such as rep-PCR and AFLP can be used as rapid, highly discriminatory screening techniques to determine the taxonomic diversity and phylogenetic structure of bacterial populations.

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

“…1), together with data from other studies (Rademaker et al, 2000;Vauterin et al, 1995), suggest that DDH values are continuous, i.e. theoretically, every value between 0 and 100 % could be obtained in DDH experiments.…”

Brachybacterium fresconis sp. nov. and Brachybacterium sacelli sp. nov., isolated from deteriorated parts of a medieval wall painting of the chapel of Castle Herberstein (Austria).

“…The mural painting strains were first screened by REP-PCR fingerprinting to group the isolates, since it has been shown that in general REP fingerprinting is in close agreement with DNA-DNA relatedness studies (Nick et al, 1999 ;Rademaker et al, 2000). The 13 isolates showed four REP types that can be subdivided into three major groups at less than 10 % similarity (Pearson coefficient).…”

Genetic Diversity and Pathogenicity of Xanthomonas axonopodis Strains Inducing Citrus Canker Disease in Iran and South Korea

“…AFLP has proven to be useful for identifying bacterial strains at subgeneric level [5,10,11,14,15,17,18,20]. Although the results of AFLP fingerprinting are specific and show high resolution to differentiate bacterial strains at the subgeneric level, it is very clear that the efficacy of this method not only depends on the choice of a suitable restriction enzyme that cleaves the most stable site in the bacterial genome but also depends on application of suitable primer to amplify the unique fragment of bacterial genome which can differentiate one strain from the others.…”

“…Rademaker et al [17] compared AFLP, rep-PCR and DNA-DNA homology for the strains of genus Xanthomonas and observed high correlation, suggesting that genomic fingerprinting techniques truly reveal genotypic and phylogenetic relationships of organisms. Gonzalez et al [5] using AFLP distinguished pathogenic and nonpathogenic strains of X. axonopodis pv.…”