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OUTLINE.md

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Bordetella Genomics Project Outline

Revised: 2019-07-01

Project goals:

  1. Produce reference-quality genome assemblies for various Bordetella species.
  2. Look for rearrangement in genomes of other Bordetella species.
  3. Predict all possible symmetric inversions based on IS element content.
Hypothesis:

Repeat content (IS481) determines frequency/extent of genome rearrangment in Bordetella species. -- But does this explain very high rearrangement in B. pertussis specifically? or perhaps reflects (diversifying) selection pressure?

Project tasks:

  1. Assemble genomes of various species
    • B. bronchiseptica: 12
    • B. parapertussis: 15
    • B. holmesii: 14
    • B. hinzii: 3
    • B. avium: 0
    • B. trematum: 2
    • B. pertussis: All CDC available (n=469)
  2. Phylogeny
    • Genus: mash + mashtree (NJ)
    • Within species: kSNP3. Compare pairwise SNP distributions within each species
  3. Whole-genome alignment within each species.
    • progressiveMauve (sw=16, hmm=0.85)
    • Identify rearrangements.
      • Yes/no, genes at boundaries, etc.
      • Circos plots
  4. Repeat content within genomes.
    • k-mer frequency distribution (jellyfish)
    • ortholog frequency (cdhit-est)
      • match ISE stability among genomes?