Bioinformatics and Evolutionary Genomics

Course goals

At the end of the course, students are expected to be able to…

1. … reconcile gene trees in terms of duplications, losses, horizontal gene transfer, endosymbiosis and lack of phylogenetic signal
2. … find homologs and assign orthologs and paralogous relations to genes
3. … understand how large scale orthology methods work and also how evolutionary processes such as gene loss, highly divergent sequences and gene fusions lead to problems for these methods.
4. … give examples how deep homology detection has changed our view on genome evolution
5. … summarize the key elements in the transition of prokaryotes to eukaryotes
6. … understand how genomic information is leveraged to detect ancient whole genome duplication events
7. …describe how function of proteins evolves after gene duplication yet is generally conserved between orthologs
8. …understand how high-throughput data on gene function can in principle be used to study evolution of function
9. … be able to read and discuss bioinformatic research papers on the interplay between genome evolution and gene function

Content

The sequencing revolution is rapidly charting ever more obscure branches in the tree of life. All these novel genomes and increasingly sophisticated bioinformatic methods are changing our view of where the complexity in our protein complexes come from and how the genes in the human genome came from. For example when we trace compare the subunits of many protein complex, it seems they are much older than originally anticipated and that genomic differences between humans and baker’s yeast are the result of massive gene loss in fungi in addition to innovations in the animal and vertebrate genomes.

In this course we will learn how novel data, novel methods  and novel concepts are driving this novel view of genome evolution. You will learn how to infer the evolutionary history of genes and proteins interest, utilizing basic (online) bioinformatic tools and your newly acquired knowledge of the interplay between genome evolution and function. The course consists of lectures, (computer) exercises and literature discussions. The first three days are focused on methods and concepts to describe genome evolutionary events. The remaining days are focused on important evolution and function events (such as the origin of eukaryotes or the whole genome duplication at the base of vertebrates) that have left their trace in e.g. the human genome.