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Computational Systems-Biology and Bioinformatics

Volume 115 of the series Communications in Computer and Information Science pp 165-179

Design of an Enterobacteriaceae Pan-Genome Microarray Chip

  • Oksana LukjancenkoAffiliated withCenter for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark
  • , David W. UsseryAffiliated withCenter for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark

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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.

Keywords

Enterobacteriaceae Pan-genome DNA microarray analysis gene Escherichia coli