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Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
Konstantinos Kritsas1, Samuel E Wuest, Daniel Hupalo
1Institute of Plant Biology & Zürich-Basel Plant Science Center, University Zürich, CH-8008 Zürich, Switzerland.
Genome Research
|September 19, 2012
Summary
Researchers discovered ultraconserved elements-like elements (ULEs) in plant genomes, which are highly conserved DNA sequences. These ULEs, found in intergenic and intronic regions, show strong purifying selection, suggesting a functional role in plants.
Area of Science:
- Genomics
- Comparative genomics
- Evolutionary biology
Background:
- Ultraconserved elements (UCEs) are DNA sequences with high similarity across species, implicated in gene regulation and genome integrity.
- The function and evolutionary pressure behind UCEs remain unclear, especially in non-mammalian species.
- Previous studies focused on UCEs in mammals, leaving their presence and role in plant genomes unexplored.
Purpose of the Study:
- To identify and characterize highly conserved DNA elements in plant genomes.
- To investigate if these elements share properties with mammalian UCEs.
- To explore the potential function and evolutionary significance of these plant UCE-like elements (ULEs).
Main Methods:
- Comparative genomic analysis of *Arabidopsis thaliana* and *Vitis vinifera* (diverged ~115 Mya).
- Identification of conserved elements >55 bp with ≥85% similarity.
- Comparative genomic analysis of *Brachypodium distachyon* and *Oryza sativa* (diverged ~50 Mya).
Main Results:
- Discovery of 36 UCE-like elements (ULEs) in *A. thaliana* and *V. vinifera* genomes.
- ULEs are located in intergenic/intronic regions, depleted from segmental duplications, and under strong purifying selection.
- ULEs exhibit reduced A+T content at borders and are located near transcription factor and developmental genes, similar to mammalian UCEs.
- A distinct set of ULEs with similar properties was identified in monocot species (*B. distachyon* and *O. sativa*).
Conclusions:
- Plant genomes harbor UCE-like elements (ULEs) with characteristics analogous to mammalian UCEs.
- The strong purifying selection on ULEs suggests significant functional roles in plants.
- The identification of ULEs provides a new avenue for investigating genome function, integrity, and regulation in plants.
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