Related Experiment Videos
A systematic search for positive selection in higher plants (Embryophytes).
Christian Roth1, David A Liberles
1Computational Biology Unit, BCCS, University of Bergen, 5020 Bergen, Norway. chregu@ii.uib.no
BMC Plant Biology
|June 21, 2006
Summary
Positive selection drives plant genome evolution, impacting key functions like defense and embryogenesis. This study reveals structural patterns of selection across diverse gene families in Embryophytes.
Area of Science:
- Plant genomics
- Evolutionary biology
- Molecular evolution
Background:
- A database of Embryophyte gene families with evidence of positive selection (Ka/Ks>>1) was previously established.
- 138 gene family branches were identified as candidates for functional adaptation.
Purpose of the Study:
- To investigate the molecular basis of plant genome evolution.
- To further analyze gene family lineages showing positive selection.
Main Methods:
- Neutral modeling to assess selection against a neutral expectation.
- Analysis of Ka/Ks ratios across protein structures.
- Reconstruction of gene families to the common ancestor of flowering plants.
Main Results:
- An excess of positive and/or negative selection was observed compared to neutral expectations.
- 490 out of 673 gene families showed evidence of positive selection within specific protein regions.
- Positive selection was detected in gene families involved in self-incompatibility, defense, embryogenesis, cold acclimation, and electron transport.
- Selective pressures varied structurally, with differences between alpha-helices, beta-sheets, and protein surfaces.
Conclusions:
- Positive selection significantly impacts a nonrandom subset of embryophyte gene families.
- More sensitive detection methods revealed a higher prevalence of positive selection.
- Structural analysis provides insights into the role of positive selection in shaping plant genomes.