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The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana
Steven Lockton1, Brandon S Gaut
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA. slockton@gmail.com
Journal of Molecular Evolution
|January 7, 2009
Summary
Transposable elements (TEs) have significantly impacted Arabidopsis thaliana protein-coding genes. Our study found TEs contributed to 1.2% of expressed genes, influencing protein function and evolution.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Transposable elements (TEs) are mobile genetic sequences.
- Their role in shaping protein-coding regions is not fully understood.
- Arabidopsis thaliana provides a model system to study TE-gene interactions.
Purpose of the Study:
- To quantify the contribution of TEs to protein-coding regions in Arabidopsis thaliana.
- To investigate the functional and evolutionary implications of TE-gene chimerism.
- To determine the directionality of TE-gene sequence similarity.
Main Methods:
- Genome-wide comparison of TE database with annotated coding sequences and EST data.
- Analysis of TE distribution within exons and introns.
- Functional enrichment analysis using Gene Ontology (GO).
- Phylogenetic analysis to infer TE-gene evolutionary relationships.
Main Results:
- 7.8% of expressed Arabidopsis genes showed similarity to known TE sequences.
- Specific TE families (Copia-like, En/Spm-like) were overrepresented in exons, while others (helitrons) were underrepresented.
- Genes with TE similarity were enriched for kinase activity and depleted for structural molecule activity.
- Phylogenetic analysis confirmed TE contributions to protein sequences in some cases.
- TEs may have contributed segments to up to 1.2% of expressed genes.
Conclusions:
- Transposable elements have played a notable role in the evolution of Arabidopsis protein-coding genes.
- TE integration can influence gene function, particularly in areas like kinase activity.
- TEs have contributed novel protein segments, expanding the functional repertoire of genes.
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