Lateral gene transfer, rearrangement, reconciliation.
BMC Bioinformatics
|February 26, 2014
Summary
We developed DeCoLT, a novel algorithm for reconstructing ancestral genome organization. It incorporates lateral gene transfer and gene family evolution, enabling the detection of co-transferred gene clusters in bacterial genomes.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Existing ancestral gene order reconstruction models overlook lateral gene transfer (LGT).
- LGT significantly impacts unicellular organism evolution and gene function discovery.
- LGT can be identified through the transfer of gene clusters.
Purpose of the Study:
- To develop an algorithm for reconstructing ancestral genome organization.
- To incorporate gene duplication, loss, and lateral gene transfer into ancestral reconstruction.
- To detect co-transferred gene clusters.
Main Methods:
- Developed DeCoLT algorithm and implementation.
- Reconstructed ancestral genomes using reconciled gene trees.
- Optimized for rearrangements (adjacency gains/breakages) in polynomial time.
- Applied to 1099 gene families across 36 cyanobacteria genomes.
Main Results:
- DeCoLT successfully reconstructed adjacencies in 35 ancestral bacterial genomes.
- The algorithm processed thousands of gene families within hours.
- DeCoLT identified clusters of co-transferred genes.
Conclusions:
- DeCoLT effectively reconstructs ancestral bacterial genomes and detects LGT events.
- The algorithm is adaptable for reconstructing ancestral interactions, functions, or complexes beyond gene adjacencies.
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