genome sequencing and annotation
DESCRIPTION
Pathogenomics research overview. Steps. Limitations. Genome sequencing and annotation. (Conserved) hypotheticals and misannotation next-gen sequencing problems with “ mobilome ”. Comprehensive identification of virulence gene candidates by various means. - PowerPoint PPT PresentationTRANSCRIPT
Genome sequencing and annotation
Comprehensive identification of virulence gene candidates by various means
Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors
Experimental determination of functions of individual virulence factors
Integrate knowledge of factors for use in:
-eco-evo-systems biology study of pathogen
-comparative genomics
“Characterization bottleneck”
Pathogenomics research overview
Steps Limitations
(Conserved) hypotheticals and misannotationnext-gen sequencing problems with “mobilome”
Ongoing curation
Protein structure/function prediction
Bioinformatic and experimental screens
Andrews-Polymenis et al. 2009
Vivo
Sassetti and Rubin 2002
Wolfgang et al. 2003
Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa
rpoS was downregulated in biofilm
Whiteley et al. 2001
Gene expression in Pseudomonas aeruginosa biofilms
Rediers et al. 2005
Valdivia and Falkow 1997
Fluorescence-based isolation of bacterial genes expressed within host cells
Valdivia and Falkow 1997
Chang et al. 2005
A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae
Lindeberg et al. 2006
Collmer et al. 2002
Tobe et al. 2006
An extensive repertoire of type III secretion effectors in Escherichia coli O157
Mazurkiewicz et al. 2006
Signature-tagged mutagenesis
Mazurkiewicz et al. 2006
TraSH = Transposon site hybridization
Mazurkiewicz et al. 2006
Jacobs et al. 2003
Comprehensive transposon mutant library of Pseudomonas aeruginosa
Jacobs et al. 2003
Jacobs et al. 2003
Comprehensive transposon mutant library of Pseudomonas aeruginosa
Medini et al. 2008
Medini et al. 2008
Metzker 2010
Langridge et al. 2009
Langridge et al. 2009
Sorek and Cossart 2010
Sorek and Cossart 2010
Sorek and Cossart 2010
Chain et al. 2009
Chain et al. 2009
Howe et al. 2008