Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the
James C Schnable1, Brent S Pedersen, Sabarinath Subramaniam
1Department of Plant and Microbial Biology, University of California Berkeley Berkeley, CA, USA.
Frontiers in Plant Science
|May 31, 2012
Summary
Whole genome duplications (tetraploidies) lead to gene loss, with conserved noncoding sequences (CNSs) influencing gene retention. Genes with more CNSs, potentially involved in dose-sensitive DNA interactions, are more likely to be retained after tetraploidy.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Whole genome duplications (WGDs), or tetraploidies, increase gene content but are followed by biased gene loss.
- Genes involved in dose-sensitive protein-protein interactions and transcription factors are preferentially retained after WGDs.
- Previous explanations for gene retention focused on protein-protein interactions.
Purpose of the Study:
- To investigate the role of conserved noncoding sequences (CNSs) in gene retention following WGDs.
- To explore the influence of dose-sensitive protein-DNA interactions on gene retention.
- To test the hypothesis that CNS quantity predicts gene retention likelihood.
Main Methods:
- Analysis of grass genomes to assess gene retention following tetraploidy events.
- Quantification of conserved noncoding sequences (CNSs) associated with genes.
- Comparison of CNSs in retained versus lost gene duplicates.
Main Results:
- The quantity of CNSs associated with a gene significantly predicts its retention likelihood after WGD.
- Genes with more CNSs are preferentially retained, suggesting a role for regulatory elements.
- Differential loss of CNSs from one gene copy in a duplicated pair reduces its retention probability in subsequent WGD events.
Conclusions:
- Conserved noncoding sequences (CNSs) play a crucial role in gene retention following whole genome duplications.
- Dose-sensitive protein-DNA interactions involving CNSs likely influence the retention of 'bigfoot genes' (CNS-rich genes).
- The evolutionary history of CNSs impacts the fate of duplicated genes in subsequent polyploidization events.
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