Abstract
Bacterial genome sequencing has developed rapidly in the last decade and has become a primary method for analyzing the genomic basis of differences in phenotype between strains as well as being a valuable tool for public health epidemiology. This chapter provides a comprehensive workflow for bacterial genome sequencing from experimental design to data suitable for comparative genomics analysis, while mainly focusing on the challenges associated with genome assembly. This approach was successfully applied to 19 Pseudomonas aeruginosa genomes from phenotypically distinct strains.
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Acknowledgements
Research in R.C. Levesque’s laboratory is funded by the Canadian Institute for Health Research (CIHR), the CIHR-Fonds de Recherche du Québec en Santé (FRQS)-Québec Respiratory Health Network (RSR) and by the Natural Sciences and Engineering Research Council of Canada (NSERC). Research in N.P. Tucker’s laboratory has been supported through grants from the Royal Society and the University of Strathclyde. N.P.T. and R.C.L. are also grateful to the Society for General Microbiology for sponsoring N.P.T. for a research visit to the corresponding author’s laboratory. J. Jeukens received a CIHR-FRQS-RSR fellowship award and was part of the Québec respiratory health training program.
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Jeukens, J., Boyle, B., Tucker, N.P., Levesque, R.C. (2014). Strategy for Genome Sequencing Analysis and Assembly for Comparative Genomics of Pseudomonas Genomes. In: Filloux, A., Ramos, JL. (eds) Pseudomonas Methods and Protocols. Methods in Molecular Biology, vol 1149. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-0473-0_43
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DOI: https://doi.org/10.1007/978-1-4939-0473-0_43
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