In this class, we will try to identify genomic islands (GI; DNA containing multiple genes that are often transferred between bacterial strains) and track down when and how these were transferred.
Before working on the project, students should take a tutorial class (available here) to familiarize themselves about bioinformatics of comparative genomics and how to use the BIOiPLUG cloud platform.
We will use the same data set as “Vibrio cholerae tutorial set”. Please provide the answers to the following questions:
We will assume that dendrogram based on ANI (average nucleotide identity) reflects the real phylogeny.
It seems that the 7th pandemic strains are monophyletic (having a common ancestor). Find GIs (consecutive gene cluster with >= 5 genes) that are only present in the 7th pandemic strains. What is the reason for that these GIs are present only in the 7th pandemic strains, but not in the other strains? What are the functions of genes in GIs? What would be a possible hypothesis of the lateral gene transfer?
Same question as question #1, but in the case of the 6th pandemic strains.
Same question as question #1, but in the case of both the 6th & 7th pandemic strains which are monophyletic (=having the same common ancestor).
Name the GIs that you found (e.g. GI #1) and draw a figure showing evolutionary history/path of GI transfers. The figure should be similar to Figure 4 of Chun et al. paper.
Last updated Sept 10, 2017 (JC)