Statistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods

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dc.contributor.authorHo Won Chang-
dc.contributor.authorYoung Do Nam-
dc.contributor.authorMin-Yeong Jung-
dc.contributor.authorKyung Ho Kim-
dc.contributor.authorSung Un No-
dc.contributor.authorMin-Su Kim-
dc.contributor.authorC O Jeon-
dc.contributor.authorJung-Hoon Yoon-
dc.contributor.authorJin-Woo Bae-
dc.date.accessioned2017-04-19T09:12:04Z-
dc.date.available2017-04-19T09:12:04Z-
dc.date.issued2008-
dc.identifier.issn01677012-
dc.identifier.uri10.1016/j.mimet.2008.08.003ko
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/8672-
dc.description.abstractThe genomic DNA-DNA hybridization (DDH) method has been widely used as a practical method for the determination of phylogenetic relationships between closely related biological strains. Traditional DDH methods have serious limitations including low reproducibility, a high background and a time-consuming procedure. The DDH method using a genome-probing microarray (GPM) has been recently developed to complement conventional methods and could be used to overcome the limitations that are typically encountered. It is necessary to compare the GPM-based DDH method to the conventional methods before using the GPM for the estimation of genomic similarities since all of the previous scientific data have been entirely dependent on conventional DDH methods. In order to address this issue we compared the DDH values obtained using the GPM, microplate and nylon membrane methods to multi-locus sequence typing (MLST) data for 9 Salmonella genomes and an Escherichia coli type strain. The results showed that the genome similarity values and the degrees of standard deviation obtained using the GPM method were lower than those obtained with the microplate and nylon membrane methods. The dendrogram from the cluster analysis of GPM DDH values was consistent with the phylogenetic tree obtained from the multi-locus sequence typing (MLST) data but was not similar to those obtained using the microplate and nylon membrane methods. Although the signal intensity had to be maximal when the targets were hybridized to their own probe, the methods using membranes and microplates frequently produced higher signals in the heterologous hybridizations than those obtained in the homologous hybridizations. Only the GPM method produced the highest signal intensity in homologous hybridizations. These results show that the GPM method can be used to obtain results that are more accurate than those generated by the other methods tested.-
dc.publisherElsevier-
dc.titleStatistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods-
dc.title.alternativeStatistical superiority of genome-probing microarrays as genomic DNA-DNA hybridization in revealing the bacterial phylogenetic relationship compared to conventional methods-
dc.typeArticle-
dc.citation.titleJournal of Microbiological Methods-
dc.citation.number3-
dc.citation.endPage530-
dc.citation.startPage523-
dc.citation.volume75-
dc.contributor.alternativeName장호원-
dc.contributor.alternativeName남영도-
dc.contributor.alternativeName정민영-
dc.contributor.alternativeName김경호-
dc.contributor.alternativeName노성운-
dc.contributor.alternativeName김민수-
dc.contributor.alternativeName전체옥-
dc.contributor.alternativeName윤정훈-
dc.contributor.alternativeName배진우-
dc.identifier.bibliographicCitationJournal of Microbiological Methods, vol. 75, no. 3, pp. 523-530-
dc.identifier.doi10.1016/j.mimet.2008.08.003-
dc.subject.keywordDNA-DNA hybridization-
dc.subject.keywordgenome-probing microarray-
dc.subject.keywordmulti-locus sequence typing (MLST)-
dc.subject.localDNA-DNA hybridization-
dc.subject.localgenome-probing microarray-
dc.subject.localmulti-locus sequence typing (MLST)-
dc.description.journalClassY-
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