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CEGA--a catalog of conserved elements from genomic alignments
Aline Dousse1, Thomas Junier1, Evgeny M Zdobnov2
1Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
Nucleic Acids Research
|November 4, 2015
Summary
Comparative genomics identifies conserved non-coding sequences (CNCs) across species. The CEGA resource catalogs these functional elements, aiding in the discovery of novel genomic functions.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Comparative genomics reveals functionally constrained genomic regions beyond annotated genes, termed conserved non-coding sequences (CNCs) or ultra-conserved elements (UCEs).
- These regions are largely uncharacterized but likely include crucial regulatory elements like enhancers and promoters.
- Understanding CNCs is vital for a comprehensive view of genome function.
Purpose of the Study:
- To introduce CEGA (Conserved Elements from Genomic Alignments), a comprehensive resource for identifying and studying CNCs.
- To facilitate the discovery of putatively functional genomic elements using cross-species conservation.
- To provide a web-based platform for exploring conserved elements across vertebrate lineages.
Main Methods:
- Utilizing multiple species comparisons to detect genomic elements under purifying selection.
- Employing threshold-free phylogenetic modeling on global alignments of synteny blocks derived from protein orthology.
- Identifying CNCs independently across five distinct vertebrate clades.
Main Results:
- Identification of millions of CNCs across different vertebrate clades, with varying numbers depending on the evolutionary radiation (e.g., 24,488 in vertebrates, 612,364 in Euarchontoglires).
- Detection of conserved elements spanning significant genomic distances, from 6 Mbp in vertebrates to 119 Mbp in Euarchontoglires.
- Development of a dynamic web interface (http://cega.ezlab.org) for visualizing alignments, locations, and associated biological data.
Conclusions:
- CEGA provides a valuable, comprehensive resource for exploring conserved non-coding sequences across vertebrates.
- The identified CNCs represent a rich source for discovering novel functional genomic elements and understanding evolutionary constraints.
- The CEGA web interface empowers researchers to prioritize and investigate specific CNCs for functional studies.
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