REGEN: Ancestral genome reconstruction for bacteria

Genes

Volumn 3, Issue 3, 2012, Pages 423-443

  Yang, Kuan ^a   Heath, Lenwood S ^b   Setubal, João C ^a,c  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b Virginia Polytechnic Institute and State University   (United States)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Bacterial genome reconstruction; Evolutionary bioinformatics; Neighboring gene pairs; Phylogeny

Indexed keywords

ANCESTRAL GENOME; ARTICLE; BACTERIAL GENOME; BIOINFORMATICS; CONTIGUOUS GENE RUN; GENE CONTENT; GENE DELETION; GENETIC PARAMETERS; GENOME ANALYSIS; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; NEIGHBORING GENE PAIR; NONHUMAN; ORTHOLOGY; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; RECONSTRUCTION OF GENOMES; REPLICON; REPLICON FISSION; REPLICON FUSION; REPLICON STRUCTURE; RHIZOBIALES; SIMULATION; TAXONOMY;

EID: 84865076321     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes3030423     Document Type: Article

References (28)

1. Boussau, B.; Karlberg, E.O.; Frank, A.C.; Legault, B.A.; Andersson, S.G. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc. Natl. Acad. Sci. USA 2004, 101, 9722-9727.
2. Slater, S.C.; Goldman, B.S.; Goodner, B.; Setubal, J.C.; Farrand, S.K.; Nester, E.W.; Burr, T.J.; Banta, L.; Dickerman, A.W.; Paulsen, I.; et al. Genome sequences of three agrobacterium biovars help elucidate the evolution of multi-chromosome genomes in Bacteria. J. Bacteriol. 2009, 191, 2501-2511.
3. Sankoff, D.; Rousseau, P. Locating the vertices of a Steiner tree in an arbitrary metric space. Math. Progr. 1975, 9, 240-246.
4. Fitch, W.M. Toward defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 1971, 20, 406-416.
5. Bhutkar, A.; Gelbart, W.M.; Smith, T.F. Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study. Genome Biol. 2007, 8, doi:10.1186/gb-2007-8-11-r236.
6. Pe'er, I.; Shamir, R. The median problems for breakpoints are NP-complete. Electron. Colloq. Comput. Complex. 1998, 71, TR98-07.
7. Moret, B.M.E.; Tang, J.; Wang, L.S.; Warnow, T. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 2002, 65, 508-525.
8. Caprara, A. Formulations and Hardness of Multiple Sorting by Reversals. In Proceedings of the 3rd International Conference of Computational Molecular Biology, Lyon, France, 11-14 April 1999; Istrail, S., Pevzner, P., Waterman, M., Eds.; ACM Press: New York, USA, 1999; pp. 84-9
9. Moret, B.M.E.; Tang, J.; Warnow, T.; Gascuel, O., Reconstructing phylogenies from gene-content and gene-order data. In Mathematics of Evolution and Phylogeny; Oxford University Press: Oxford, UK, 2005; Chapter 12, pp. 321-352.
10. Bourque, G.; Tesler, G.; Pevzner, P.A. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 2006, 16, 311-313.
11. Eriksen, N. Reversal and transposition medians. Theor. Comput. Sci. 2007, 374, 111-126.
12. Yang, K.; Setubal, J.C. Homology Prediction Refinement and Reconstruction of Gene Content and Order of Ancestral Bacterial Genomes. In Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, Niagara Falls, NY, USA, 2-4 August 2010; Zhang, A., Borodovsky, M., Eds.; ACM: New York, NY, USA, 2010; pp. 230-236. Available online: http://dl.acm.org (accessed on 10 July 2012).
13. Yang, K.; Setubal, J.C. A Whole Genome Simulator of Prokaryote Genome Evolution. In Proceedings of the Second ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Chicago, IL, USA, 31 July-3 August 2011; Grossman, R., Rzhetsky, A., Eds.; ACM: New York, NY, USA, 2011; pp. 508-510. Available online: http://dl.acm.org (accessed on 10 July 2012).
14. The Setubal Research Group. Available online: http://staff.vbi.vt.edu/jcslab/tools.html (accessed on 1 July 2012).
15. Price, M.N.; Huang, K.H.; Alm, E.J.; Arkin, A.P. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucl. Acids Res. 2005, 33, 880-892.
16. Stamatakis, A. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22, 2688-2690.
17. Li, L.; Stoeckert, C.J., Jr; Roos, D.S. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13, 2178-2189.
18. Buschbom, J.; Barker, D. Evolutionary history of vegetative reproduction in porpidia s.l. (lichen-forming ascomycota). Syst. Biol. 2006, 55, 471-484.
19. Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 2000, 28, 27-30.
20. De Queiroz, A.; Gatesy, J. The supermatrix approach to systematics. Trends Ecol. Evol. 2007, 22, 34-41.
21. Altschul, S.F.; Madden, T.L.; Schffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 1997, 25, 3389-3402.
22. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32, 1792-1797.
23. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17, 540-552.
24. Alexeyenko, A.; Tamas, I.; Liu, G.; Sonnhammer, E.L. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 2006, 22, e9-e15.
25. Kruskal, J. On the shortest spanning subtree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 1956, 7, 48-50.
26. Cormen, T.; Leiserson, C.; Rivest, R.; Stein, C. Introduction to Algorithms; McGraw-Hill: New York, NY, USA, 2003.
27. Harrison, P.W.; Lower, R.P.J.; Kim, N.K.D.; Young, J.P.W. Introducing the bacterial 'chromid': Not a chromosome, not a plasmid. Trends Microbiol. 2010, 18, 141-148.
28. Wu, D.; Hugenholtz, P.; Mavromatis, K.; Pukall, R.; Dalin, E.; Ivanova, N.N.; Kunin, V.; Goodwin, L.; Wu, M.; Tindall, B.J.; et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462, 1056-1060.