Bioinformatic exercise
· interpret annotation cautiously
o start sites
o operons, 50bp rule of thumb
· check alignments and E values
· be suspicious

Lecture 1 Intro
· what is virulence lifestyle?
· genomics enables more accurate phylogenetic analysis
· core vs. flexible genome

Lecture 2 Tools: Information theory and BLAST
· choosing proper BLAST matrices, tools, web sites, etc.
· bringing together worlds of sequence analysis and biological knowledge

Lecture 3 Tools: Omics
· microarrays, IVET, and other global clues to function
· overall strategy for functional genomics

Lecture 4 Xylella and Xanthomonas. spp.
· from blackbox to many credible hypotheses
· different virulence systems may be involved in host specificity

Lecture 5 Horizontal gene transfer
· multiple mechanisms and prevalence
· distinct evolution of core and flexible genome
· conjugation and phage mediated
· transposition and IS elements
· Campbell integration

Lecture 6 0157:H7 and E. carotovora
· pathogenicity islands acquired via phage integration
· TTSS master virulence system and horizontally acquired
· evolution of virulence systems in E. coli lineages
· O and K islands

Lecture 7 Yersinia
· Y. pestis and punctuated equilibrium
· the paradigm TTSS with well defined effector and translocator Yops
· independent acquisition of TTSS by different pathogenic species
· Yersinia genome rearrangement frequent
· Y. pestis = 2 new plasmids and many pseudogenes

Lecture 8 Ralstonia
· Interesting genome structure
· ancient TTSS and unusual lack of R gene resistance in (numerous) hosts
· redundancy in function of TTSS effectors

Lecture 9 Rhizobiaceae
· core genome and large plasmids with host-interaction factors
· nod genes transmissible on plasmids or ICElands
· paradigm type IV secretion system

Lecture 10 Pseudomonas
· microrarray analysis of PAO1 genome and clinical isolates reveals mostly core genome and hotspots for indels
· use of multikingdom pathogen to study virulence determinants in burned animals using plant bioassays