PT  - JOURNAL ARTICLE
AU  - Nguyen, Huy N.
AU  - Jain, Ashish
AU  - Eulenstein, Oliver
AU  - Friedberg, Iddo
TI  - Ancestral Reconstruction of Gene Blocks using an Event-Based Method
AID  - 10.1101/212886
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 212886
4099  - http://biorxiv.org/content/early/2017/11/01/212886.short
4100  - http://biorxiv.org/content/early/2017/11/01/212886.full
AB  - Motivation A fundamental attribute of life is complex systems: systems made of parts that together perform functions that a single component, or most subsets containing individual components, cannot. Examples of molecular complexity include protein structures such as the F1F0-ATPase, the ribosome, or the flagellar motor. Each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are a classic example of a complex system. An operon's genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule. The operon's gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to examine the evolution of operons and identify possible intermediate states.Results In this work, we used a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We offer the software as the Reconstruction of Ancestral Genomes Using Events or ROAGUE.Availability and implementation The software is available on https://github.com/nguyenngochuy91/Ancestral-Blocks-ReconstructionContact huyn{at}iastate.edu, idoerg{at}iastate.edu