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REGEN: Ancestral Genome Reconstruction for Bacteria
Kuan Yang1, Lenwood S Heath2, João C Setubal3
1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. yangkuan81@gmail.com.
Genes
|April 8, 2014
Summary
REGEN reconstructs ancestral bacterial genomes, detailing gene content and evolutionary events like gene gain/loss and replicon fusion/fission. This computational system enhances phylogenetic studies for bacteria.
Area of Science:
- Computational Biology
- Genomics
- Evolutionary Biology
Background:
- Traditional phylogenetic trees offer limited detail for evolutionary studies.
- Ancestral genome reconstruction requires detailed analysis of gene content and genomic structures.
Purpose of the Study:
- To introduce REGEN, a novel computational system for ancestral bacterial genome reconstruction.
- To reconstruct gene content, gene order, and replicon structure for ancestral bacterial genomes.
- To infer evolutionary events along phylogenetic branches, including gene and replicon dynamics.
Main Methods:
- REGEN utilizes a neighboring gene pair approach for gene content reconstruction.
- Employs maximum parsimony or maximum likelihood methods for reconstruction.
- Infers evolutionary events such as gene creation/deletion and replicon fission/fusion.
Main Results:
- Successfully reconstructed ancestral bacterial genomes at gene and replicon levels.
- Demonstrated capability in inferring gene content, gene runs, and replicon organization.
- Validated REGEN's performance on simulated data and bacterial genomes from the Rhizobiales order.
Conclusions:
- REGEN provides a detailed approach to ancestral genome reconstruction, enhancing phylogenetic insights.
- The system is applicable to related bacterial genomes, typically within the same taxonomic order.
- REGEN advances the study of bacterial evolution by reconstructing ancestral genomic states and events.
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