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Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton
Lex E Flagel1, Jonathan F Wendel
1Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
The New Phytologist
|December 17, 2009
Summary
Gene expression evolution in cotton allopolyploids reveals conserved biases and surprising regulation changes. This study tracks expression changes after genome duplication, offering insights into polyploid evolution.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Science
Background:
- Allopolyploidy, the duplication of entire genomes from different species, is a major evolutionary force in plants.
- Understanding gene expression evolution after polyploidization is crucial for deciphering plant adaptation and diversification.
Purpose of the Study:
- To investigate the temporal patterns of gene expression evolution in five allopolyploid cotton (Gossypium) species following a shared genome duplication event.
- To compare expression changes in natural allopolyploids with those in synthetic F(1) hybrids to understand the impact of polyploidy on gene regulation.
Main Methods:
- Utilized a custom microarray to measure global gene expression in petal RNAs from five allopolyploid Gossypium species.
- Quantified total expression for approximately 42,000 duplicated genes and genome-specific expression for about 1,400 homoeologs.
- Employed a phylogenetic framework to analyze expression diversification over time and compared patterns with F(1) hybridization.
Main Results:
- Observed a consistent homoeolog expression bias favoring the D genome over the A genome across all studied allopolyploid species (54-60%).
- Identified significant transgressive up- and down-regulation of genes in allopolyploids.
- Noted a reduction in the level of bias in genomic expression dominance, but not its magnitude, and high interspecific rate variation in expression evolution.
Conclusions:
- Gene expression evolution in Gossypium allotetraploids shows overall similarity despite high interspecific rate variation.
- Expression patterns in natural allopolyploids diverge significantly from those observed in synthetic F(1) hybrids, highlighting the unique evolutionary trajectory post-polyploidization.
- The study provides a temporal perspective on expression diversification following allopolyploidy, partitioning phylogenetic and temporal components of evolution.
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