Exercises: Whole Genome Duplications

  1. genome duplications in yeast

    1. Go to the yeast gene order browser. Search for RPL27A (you can do this in the field next to the button named browse).
    2. Which S.cerevisiae relatives have two copies of RPL27A and which have one?
    3. We can align the S.cerevisiae chromosomal region from RPL27a-DIA4-VPS29 and TLG1-SDC1-UGO1-RPL27B fully to a single chromosomal region in most of the pre-genome duplication yeast species. Sketch such an alignment for one such pre-WGD species and the regions in cerevisiae.
    4. How many genes were lost from either or both of these two paralogous stretches in the lineage leading to S. cerevisiae? (i.e. stretch means from VPS29 to TLG1).
    5. Search the YGOB for mad3 and/or for bub1. Which species has/ve a single madbub protein, even though they are post whole genome duplication. What would that suggest about its domain composition given the introductory lectures. lecture tree basics from master course introduction to bioinformatics?
    6. What where thus the two different fates of the madbub after the WGD? Check your hypothesis in this preview by Andrew Murray.
  2. genome duplications in vertebrates

    1. Look at the tree in panel A of the figure given here. In what way did these paralogs functionally differentiate?
    2. These duplications from the tree look like the result of the genome duplication at the base of the vertebrates. The following paper describes a webtool that integrates phylogenetic and synteny information to infer whether a vertberate gene is the result of the WGD: ohnologs.curie. The paper can be found here. Search for "PFKFB1" and see to what extend the gene tree is the result of a WGD according to this analysis.
    3. How do you think this webserver compares to YGOB. What potentially explains the difference? (Also take into account figure 1 and figure 2 from the ohnolog.curie paper).