Experimental error in DNA–DNA pairing: a survey of the literature

Hartford, T.; Sneath, P. H. A.

doi:10.1111/j.1365-2672.1990.tb05218.x

Cited by 10 publications

(12 citation statements)

References 51 publications

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“…The correlation between duplicate DNA-DNA homology series (n l 751) was found to be 0n942, with the same level of significance (P l 0n0001 ; for a survey of the literature on experimental error in DNA-DNA pairing, see Hartford & Sneath, 1990). The correlation of the combined BER fingerprint similarities with DNA-DNA homology values (0n808) was found to be higher than those found with individual BOX (0n779), ERIC (0n669) or REP (0n777) data sets.…”

Section: Cluster Analysis Of Rep-pcr Genomic Fingerprints Versus Dna-mentioning

confidence: 73%

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

Rademaker¹,

Hoste²,

Louws³

et al. 2000

International Journal of Systematic and Evolutionary Microbiology

319

245

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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.

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Section: Cluster Analysis Of Rep-pcr Genomic Fingerprints Versus Dna-mentioning

confidence: 73%

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

Rademaker¹,

Hoste²,

Louws³

et al. 2000

International Journal of Systematic and Evolutionary Microbiology

319

245

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“…Levels of error in replication experiments were measured as the standard deviations for the DNA-DNA pairing values for each pair of strains (6). Pairing values were divided into 10 bands at 10% intervals, and the errors were averaged over each 10% range.…”

Section: Resultsmentioning

confidence: 99%

“…The level of error seemed to be independent of the percentage of pairing, although the levels of error were higher at very low pairing values and high pairing values (more than 90%). There were no zero errors or violating triangles when we used the TRUDNA program (Leicester University Vax Cluster) (6).…”

Section: Resultsmentioning

confidence: 99%

Optical DNA-DNA Homology in the Genus Listeria

Hartford

Sneath²

1993

International Journal of Systematic Bacteriology

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Twenty-three strains of the seven recognized Listeria species were studied by using DNA-DNA optical hybridization. The level of error in the data was low. Our results supported the results of Rocourt et al. (J. Rocourt, F. Grimont, P. A. D. Grimont, and H. P. R. Seeliger, Cum. Microbiol. 7:383-388, 1982), although there was some overlap between Listeriu monocytogenes and Listeria innocuu. We suggest that there may be more than one cluster in the species L. monocytogenes or the species may form a large spectrum of relatedness. The level of intraspecies homology in L. monocytogenes is very broad, as determined in both this study and other studies. In their DNA studies, Rocourt et al. (10) divided what was the L. monocytogenes complex into the five species that are recognized today; this division was supported by a small number of biochemical differences (11). However, only six C1087T (= NCTC 11846T = ATCC 19119T = SLCC 2379T) C659 (= P L242) C663 (= P L72) C666 (= P L234) C667 (= P L102B) C214 (= SLCC 332/64) SLCC 7211 C1174T (= NCTC 10812T = ATCC 25401*)

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“…However, the practical problems connected with establishing DNA-DNA reassociation values also limit their use in general taxonomic studies for many laboratories at present (12). Furthermore, the failure of reassociation studies to give expression to low levels of homology has been noted previously (12), as have the significance of experimental error in reassociation studies and the extent to which this is ignored in the interpretation of data (12,28). Experimental error may set a limit on the utility of reassociation values in taxonomic studies until improved methods overcome this difficulty.…”

Section: Discussionmentioning

confidence: 99%

Numerical Analysis and Determinative Tests for Nonfluorescent Plant-Pathogenic Pseudomonas spp. and Genomic Analysis and Reclassification of Species Related to Pseudomonas avenae Manns 1909

Young²,

Triggs

1991

International Journal of Systematic Bacteriology

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We performed a numerical analysis of the results of biochemical and nutritional tests done with strains of nonfluorescent plant-pathogenic Pseudomonas spp. A total of 57 tests were used, and determinative tests which discriminated between taxa were identified. Pseudomonas andropogonis, P. caryophylli, P . corrugata, P . glumae, P . plantarii, and P . rubrisubalbicans were distinguished as distinct members of the genus Pseudomonas. Strains of P . Jicuserectae and P . meliae formed a single cluster having affinities with P . syringae. Strains of P . cissicola were allocated to Agrobacterium spp. Strains of P . avenae, P . cattleyae, P . pseudoalcaligenes subsp. citrulli, P . pseudoalcaligenes subsp. konjaci, and P . rubrilineans formed a single relatively homogeneous cluster, within which three subclusters were discerned. Strains presently identified as P . avenae and as P . rubrilineans, including the type strain of P . cattleyae, formed a single homogeneous subcluster. Strains of P . pseudoalcaligenes subsp. citrulli and P. pseudoalcaligenes subsp. konjaci formed two subclusters. Genomic probes prepared from DNAs of the type strains of P. avenae, P . cattleyae, P . pseudoalcaligenes subsp. citrulli, P . pseudoalcaligenes subsp. konjaci, and P . rubrilineans gave positive reactions with all of the strains of these species which were tested in colony hybridization studies, but not with strains of other nonfluorescent Pseudomonas spp. The G+C ratios of these type strains were all in the range from 67 to 71 mol%, and the levels of homology determined in DNA-DNA reassociation studies were all greater than 70%. P . avenae, P . cattleyae, P . pseudoalcaligenes subsp. citrulli, P . pseudoalcaligenes subsp. konjaci, and P . rubrilineans are considered to be members of a single species, P . avenae, with P . cattleyae and P . rubrilineans as junior synonyms; P . pseudoalcaligenes subsp. citrulli and P . pseudoalcaligenes subsp. konjaci are proposed as subspecies.The genus Pseudomonas Migula 1894, which at the present time is defined on the basis of phenetic data, is heterogeneous in its genomic relationships. An analysis of DNA-rRNA homologies has shown that the members of this genus fall into several distinct genetic groups which could be considered to be members of separate genera if the genetic data were supported by phenetic differences (21,22).Plant-pathogenic Pseudomonas spp. are distinguished according to whether they produce fluorescent pigments on iron-deficient media and produce poly-P-hydroxybutyrate inclusions (13,14 (22), are also members of this group (6).Organisms which are members of an "acidovorans" DNA-rRNA homology group (6) A numerical analysis of results of biochemical and nutritional tests performed with strains of nonfluorescent plantpathogenic Pseudomonas spp. (16) suggested that P. avenue, P. cattleyae, P. pseudoalcaligenes subsp. citrulli, and P. rubrilineans form a single homogeneous group, which was called the "avenae" cluster (16). The close relationship of the members of the avenae cluster wa...

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Experimental error in DNA–DNA pairing: a survey of the literature

Cited by 10 publications

References 51 publications

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

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

Optical DNA-DNA Homology in the Genus Listeria

Numerical Analysis and Determinative Tests for Nonfluorescent Plant-Pathogenic Pseudomonas spp. and Genomic Analysis and Reclassification of Species Related to Pseudomonas avenae Manns 1909

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