Characterization of microbial pathogens by DNA microarrays

Huyghe, Antoine; François, Patrice; Schrenzel, Jacques

doi:10.1016/j.meegid.2008.10.016

Cited by 22 publications

(11 citation statements)

References 84 publications

(90 reference statements)

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“…Comparative genomic hybridization (CGH), using such DNA array technology, has been applied for the determination of global genome variations among closely related bacteria [16]. CGH analyses of nine strains of B. japonicum were performed to clarify their genomic variations [15].…”

Section: Introductionmentioning

confidence: 99%

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

Kaneko

Maita

Hirakawa

et al. 2011

Genes

110

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The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

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Section: Introductionmentioning

confidence: 99%

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

Kaneko

Maita

Hirakawa

et al. 2011

Genes

110

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“…This technique has primarily been used to characterize gene copy number changes and deletion events and has been applied extensively in the study of human tumorogenesis and bacterial pathogens [9-14]. …”

Section: Introductionmentioning

confidence: 99%

Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach

et al. 2011

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BackgroundComparative Genomic Hybridization (CGH) with DNA microarrays has many biological applications including surveys of copy number changes in tumorogenesis, species detection and identification, and functional genomics studies among related organisms. Array CGH has also been used to infer phylogenetic relatedness among species or strains. Although the use of the entire genome can be seen as a considerable advantage for use in phylogenetic analysis, few such studies have questioned the reliability of array CGH to correctly determine evolutionary relationships. A potential flaw in this application lies in the fact that all comparisons are made to a single reference species. This situation differs from traditional DNA sequence, distance-based phylogenetic analyses where all possible pairwise comparisons are made for the isolates in question. By simulating array data based on the Neurospora crassa genome, we address this potential flaw and other questions regarding array CGH phylogeny.ResultsOur simulation data indicates that having a single reference can, in some cases, be a serious limitation when using this technique. Additionally, the tree building process with a single reference is sensitive to many factors including tree topology, choice of tree reconstruction method, and the distance metric used.ConclusionsWithout prior knowledge of the topology and placement of the reference taxon in the topology, the outcome is likely to be wrong and the error undetected. Given these limitations, using CGH to reveal phylogeny based on sequence divergence does not offer a robust alternative to traditional phylogenetic analysis.

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“…The methods described earlier may soon face the competition of new technologies like DNA microarrays or chips, in which hundreds to thousands of immobilized DNA probes are spotted or directly synthesized with a predetermined spatial arrangement on an impermeable, rigid, fl at support such as glass (e.g., see the review by Huyghe et al 86 ). Usually, robots are required to place this large number of probes onto slides.…”

Section: Gdnamentioning

confidence: 99%

“…Usually, robots are required to place this large number of probes onto slides. Although high -density microarrays have been used in applications as varied as transcriptomics, single nucleotide polymorphism (SNP) analysis, and drug discovery, 86 with the current state of the microarray technology, it is easy to envision a microarray specifi c for the detection of residual E. coli gDNA in plasmid samples, where selected probes (e.g., for the 16S ribosomal RNA gene) are attached to specifi c sites in a chip. After a series of stringent washes, the signal that results from hybridization at each spot is measured with an adequate scanner.…”

Section: Gdnamentioning

confidence: 99%

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Prazeres¹

2011

Plasmid Biopharmaceuticals

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Characterization of microbial pathogens by DNA microarrays

Cited by 22 publications

References 84 publications

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T

Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach

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