Microarray-Based Detection and Typing of the Rhizobium Nodulation Gene
            <i>nodC</i>
            : Potential of DNA Arrays To Diagnose Biological Functions of Interest

Bontemps, Cyril; Golfier, Geoffroy; Gris-Liebe, Carine; Carrère, Sébastien; Talini, Luc; Boivin-Masson, Catherine

doi:10.1128/aem.71.12.8042-8048.2005

Cited by 25 publications

(16 citation statements)

References 41 publications

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“…Recently, a model system of nodC-and nec1-targeted monitoring was developed to diagnose rhizobial function (Bontemps et al, 2005) and disease control (Koyama et al, 2007). Our CGH profiles are available to examine overall genotypic diversity, including the hup and nos genotypes of B. japonicum field isolates.…”

Section: Discussionmentioning

confidence: 99%

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

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Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G þ C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.

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Section: Discussionmentioning

confidence: 99%

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

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“…An FGA composed of probes for the nodC gene, which is a common nod gene essential for nodulation in all rhizobial species investigated so far, was developed and used to detect known and new nodC sequences [24]. One hundred thirty probes (41-and 50-mer) were designed from two conserved regions of the nodC gene.…”

Section: Fgas For Nitrogen Cyclingmentioning

confidence: 99%

Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

Nostrand

Deng

et al. 2011

Front. Environ. Sci. Eng. China

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Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus, and metals, biodegradation of environmental contaminants, energy processing, and stress responses. GeoChips are considered as the most comprehensive FGAs. Experimentally established probe design criteria and a computational pipeline integrating sequence retrieval, probe design and verification, array construction, data analysis, and automatic update are used to develop the GeoChip technology. GeoChip has been systematically evaluated and demonstrated to be a powerful tool for rapid, specific, sensitive, and quantitative analysis of microbial communities in a high-throughput manner. Several generations of GeoChip have been developed and applied to investigate the functional diversity, composition, structure, function, and dynamics of a variety of microbial communities from different habitats, such as water, soil, marine, bioreactor, human microbiome, and extreme ecosystems. GeoChip is able to address fundamental questions related to global change, bioenergy, bioremediation, agricultural operation, land use, human health, environmental restoration, and ecological theories and to link the microbial community structure to environmental factors and ecosystem functioning.

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“…The first strategy based on this principle was called COnsensus DEgenerate Hybrid Motif Oligonucleotide Probe (CODEHMOP) [26]. The first strategy based on this principle was called COnsensus DEgenerate Hybrid Motif Oligonucleotide Probe (CODEHMOP) [26].…”

Section: Iupac Code Definitionmentioning

confidence: 99%

High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

Jaziri

Peyretaillade

Peyret

et al. 2014

Concurrency and Computation

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Complete backtranslation is the step of generating all possible nucleic acid sequences from a protein sequence. This is a time-consuming task that can provide unreasonable quantities of data. Complete backtranslation was recently used to initiate probe design for functional DNA microarrays from conserved peptidic regions, in order to assess the full microbial gene diversity present in complex environments. In this article, we present an efficient parallelization method to compute a complete backtranslation of short peptides to select probes for functional microarrays. We implemented a software that uses meta-programming and a model-driven engineering approach to automatically generate source codes to perform complete backtranslation on different architectures: PCs, Symmetric Multiprocessors servers, computing clusters, or a computing grid. Our software is filtering the generated oligonucleotides with usual selection criteria for the design of microarray probes. It uses load balancing and can be easily integrated in probe design software for functional microarrays. We present its performance on both simulated and real biological datasets. The obtained results show a significant computing speedup on different platforms and an important gain of about 40% of disk space when filtering oligonucleotides.

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Microarray-Based Detection and Typing of the Rhizobium Nodulation Gene nodC : Potential of DNA Arrays To Diagnose Biological Functions of Interest

Cited by 25 publications

References 41 publications

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities

High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

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