Ancestral Reconstruction of Gene Blocks using an Event-Based Method

Abstract

Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets containing individual components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-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 operons genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operons gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons. In this work, we developed 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 describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution.\n\nThe software accompanying this paper is available under GPLv3 license in: https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction.\n\nAll figures in this paper are available in enlarged downloadable form from:https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction/tree/master/images