Abstract
Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.
Highlights
Ancestral genome reconstruction can be understood as a phylogenetic study of a set of species with more details than what is provided by a traditional phylogenetic tree
We compared reconstructions produced by the maximum parsimony (MP) and maximum likelihood (ML) methods with gene pair cutoff set to 0.75, 0.8, 0.85, 0.9, 0.95, and 0.97
In order to simplify the analysis process, we focused on the reconstructed gene runs with at least four genes for the last common ancestor (LCA) of all Rhizobiales species
Summary
Ancestral genome reconstruction can be understood as a phylogenetic study of a set of species with more details than what is provided by a traditional phylogenetic tree It may include information about ancestor species such as their gene content, the order of these genes in the genome, the replicon. That we call REGEN (REconstruction of GENomes), which includes phylogenomic tree reconstruction, ortholog identification and refinement (which uses results previously published [12]), gene content reconstruction, contiguous gene run reconstruction, and replicon architecture reconstruction. It does not include nucleotide sequence reconstruction. REGEN is open source software [14]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
