Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes

Abstract

We present a systematical methodology to refine orthologs identification generated by 3rd party de novo prediction programs and reconstruction of ancestral bacteria genome with this information by a neighboring gene pairs (NGPs) based method. The refinement method combined phylogeny and local gene synteny to improve homology prediction and the reconstruction is focused on both gene content and conserved blocks. Despite the common believe that gene order are much less conserved in prokaryotes, we have applied this method to Rhizobiales, an order of alpha proteobacteria, and show that a reasonable number of large conserved syntenic blocks can still be reconstructed.