Design of an Enterobacteriaceae Pan-genome Microarray Chip

Oksana Lukjancenko, David Ussery

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    Abstract

    Abstract. Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination of the genetic makeup of unknown strains within this bacterial family and can introduce insights into phylogenetic relationships.
    Original languageEnglish
    Title of host publicationCSBio 2010
    Volume115
    PublisherSpringer
    Publication date2010
    Pages174-189
    Publication statusPublished - 2010
    EventInternational Conference on Computational Systems-Biology and Bioinformatics : Proceedings -
    Duration: 1 Jan 2010 → …

    Conference

    ConferenceInternational Conference on Computational Systems-Biology and Bioinformatics : Proceedings
    Period01/01/2010 → …

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