Evolution of Gene Regulation Following Whole Genome Duplication in Salmonids

Explore the evolution of gene regulation following whole genome duplication in salmonids through this comprehensive seminar. Delve into the fascinating world of salmonid genomics, focusing on the Atlantic salmon as a model for genome evolution after whole genome duplication. Examine gene loss and retention patterns, tissue regulatory divergence, and the challenges of distinguishing between evolutionary scenarios. Learn about the Ornstein-Uhlenbeck model as a framework for modeling expression evolution. Investigate expression level shifts, tissue-specific evolution, and ongoing pseudogenization. Discover the role of cis-regulatory elements in duplicate expression evolution through ATAC-seq and TFBS footprinting techniques. Gain insights into how transposable elements contribute to novel adaptive expression phenotypes in salmonids. Conclude with a summary of key findings and their implications for understanding genome evolution in these economically and culturally significant fish species.

Intro
Who are the salmonids ?
The Atlantic salmon Culture and cash
Salmonids a model for genome evolution after WGD
Salmonid genomes 101
Gene loss/retention after Ss4R
Tissue regulatory divergence
How does gene regulation diverge?
Mode of tissue regulation divergence
Assymetric divergence following ancient vertebrate WGDs
A challenge... distinguishing between evolutionary scenarios
The OU-model: A framework to model expression evolution
The experiment
Tests for expression level shift
Tissue specific evolution?
Signatures of ongoing pseudogenization ?
Are particular cellular functions
Brief summary 2: expression evolution following WGD
Approach: ATAC-seq&TFBS footprinting
Sanity check = OK
Cis-regulatory evolution and tissue specificity
Does Tes contribute to novel 'adaptive' expression phenotypes?
Brief summary 3: CREs and duplicate expression evolution
Some concluding thoughts
Acknowledgements