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? (You can also scan the original publication here)
   6. What where thus the two different fates of the madbub after the WGD? Check your hypothesis in this preview by Andrew Murray.
   7. For not more than 5 minutes, try and google or search supplementary material of relevant papers to determine if something like the YGOB browser exists for vertebrates and for plants. I think not, but hopefully you can prove me wrong. In any case, reflect on why this might be the case. I think the reason is different for vertebrates than it is for plants.