General information and course material
General objectives
Understand the importance of gene and genome duplication in comparative genomics; understand the difficulty of comparing “function” between homologous genes, and know some tools to do so.
Course material
Lecture 1: Function in model vs non-model organisms
Learning outcomes
- Notion of “function” for genes
- Sources of information on functions
- Annotation and biocuration
- Transfer and reliability of annotations in non-model species
Lecture 2: Finding information about gene function at small scale
Learning outcomes
- Orthologue conjecture
- Functional enrichment
- Evolution of gene expression:
- Gene expression as a quantitative trait
- Conservation among species (clustering per organ not per species)
- Fast evolution of testis genes
- Convergent evolution: venom glands
Lecture 3: Gene and genome duplication
Learning outcomes
- Types of duplication: tandem, retroposition, whole genome
- Biased gene retention
- Evolution after duplication: sub- and neo-functionalisation
- Impact of duplication on biology:
- Large gene family expansions
- Whole genome duplications in eukaryote evolution
Course gitlab repository
The gitlab repository to run all the practicals is available at https://github.com/BgeeDB/Biodiversity-Bioinformatics.
Note
Remember to open a Gitpod workspace before starting the practicals. Click here for more information on Gitpod workspace.
Provided data files and scripts
You can find the Exercise 3 datasets here and the R script to use in Exercise 2 here.