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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

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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

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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

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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.