Towards an accurate identification of mosaic genes and partial horizontal gene transfers

Nucleic Acids Research

Volumn 39, Issue 21, 2011, Pages

  Boc, Alix ^a   Makarenkov, Vladimir ^a  

^a UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ALLELE; ARTICLE; BOOTSTRAPPING; CONTROLLED STUDY; DNA RECOMBINATION; DONOR; GENE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC MARKER; GENOME; HORIZONTAL GENE TRANSFER; HOST; HUMAN; MOSAIC GENE; MOSAICISM; NONHUMAN; PRIORITY JOURNAL; SIMULATION;

ESCHERICHIA COLI PROTEINS; GENE TRANSFER, HORIZONTAL; MONTE CARLO METHOD; MOSAICISM; PHYLOGENY; RECOMBINATION, GENETIC; RIBULOSE-BISPHOSPHATE CARBOXYLASE; SEQUENCE ALIGNMENT;

EID: 82255194354     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr735     Document Type: Article

References (50)

1. Doolittle, W.F. (1999) Phylogenetic classification and the universal tree. Science, 284, 2124-2129.
2. Koonin, E.V. (2003) Horizontal gene transfer: the path to maturity. Mol. Microbiol., 5, 725-727. (Pubitemid 37372237)
3. Doolittle, W.F., Boucher, Y., Nesbø, C.L., Douady, C.J., Anderson, J.O. and Roger, A.J. (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos. Trans. R. Soc. Lond. B. Biol. Sci., 358, 39-57.
4. Nakhleh, L., Ruths, D. and Wang, L.S. (2005) RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer. In Wang, L. (ed.), Lecture Notes in Computer Science. Springer, Kunming, China, pp. 84-93. (Pubitemid 41450189)
5. Makarenkov, V., Kevorkov, D. and Legendre, P. (2006) Phylogenetic network reconstruction approaches. Bioinformatics, 6, 61-97.
6. Boc, A., Philippe, H. and Makarenkov, V. (2010) Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst. Biol., 59, 195-211.
7. Hollingshead, S.K., Becker, R. and Briles, D.E. (2000) Diversity of PspA: mosaic genes and evidence for past recombination in Streptococcus pneumoniae. Infect. Immun., 68, 5889-5900.
8. Zhaxybayeva, O., Lapierre, P. and Gogarten, J.P. (2004) Genome mosaicism and organismal lineages. Trends Genet., 20, 254-260. (Pubitemid 38510439)
9. Gogarten, J.P., Doolittle, W.F. and Lawrence, J.G. (2002) Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol., 19, 2226-2238. (Pubitemid 35440456)
10. Lawrence, J.G. and Ochman, H. (1997) Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol., 44, 383-397. (Pubitemid 27161335)
11. Maiden, M. (1998) Horizontal genetic exchange, evolution, and spread of antibiotic resistance in bacteria. Clin. Infect. Dis., 27, 12-20.
12. Zheng, Y., Roberts, R.J. and Kasif, S. (2004) Segmentally variable genes: a new perspective on adaptation. PLoS Biol., 2, 452-464.
13. Claverys, J.P., Prudhomme, M., Mortier-Barriè re, I. and Martin, B. (2000) Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol. Microbiol., 35, 251-259. (Pubitemid 30055223)
14. Hein, J. (1993) A heuristic method to reconstructing the evolution of sequences subject to recombination using parsimony. J. Mol. Evol., 36, 396-405. (Pubitemid 23121907)
15. von Haeseler, A. and Churchill, G.A. (1993) Network models for sequence evolution. J. Mol. Evol., 37, 77-85. (Pubitemid 23174579)
16. Page, R.D.M. (1994) Maps between trees and cladistic analysis of historical associations among genes, organism and areas. Syst. Biol., 43, 58-77. (Pubitemid 24979624)
17. Mirkin, B.G., Muchnik, I. and Smith, T.F. (1995) A biologically consistent model for comparing molecular phylogenies. J. Comput. Biol., 2, 493-57.
18. Maddison, W.P. (1997) Gene trees in species trees. Syst. Biol., 46, 523-536.
19. Charleston, M.A. (1998) Jungle: a new solution to the host/parasite phylogeny reconciliation problem. Math. Biosci., 149, 191-223. (Pubitemid 28249100)
20. Hallett, M. and Lagergren, J. (2001) Efficient algorithms for lateral gene transfer problems. In El-Mabrouk, N., Lengauer, T. and Sankoff, D. (eds), Proceedings of the Fifth Annual International Conference on Research in Computational Biology. ACM Press, New York, pp. 149-156. (Pubitemid 32866153)
21. Boc, A. and Makarenkov, V. (2003) New efficient algorithm for detection of horizontal gene transfer events. In Benson, G. and Page, R. (eds), Algorithms in Bioinformatics. Springer, Budapest, Hungary, pp. 190-201.
22. MacLeod, D., Charlebois, R.L., Doolittle, F. and Bapteste, E. (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol. Biol., 5, 27.
23. Tsirigos, A. and Rigoutsos, I. (2005) A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res., 33, 922-933. (Pubitemid 41430513)
24. Tsirigos, A. and Rigoutsos, I. (2005) A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res., 33, 3699-3707. (Pubitemid 41418539)
25. Beiko, R.G. and Hamilton, N. (2006) Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol., 6, 15.
26. Jin, G., Nakhleh, L., Snir, S. and Tuller, T. (2006) Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics, 23, 123-128.
27. Jin, G., Nakhleh, L., Snir, S. and Tuller, T. (2007) Inferring phylogenetic networks by the maximum parsimony criterion. Mol. Biol. Evol., 241, 324-337. (Pubitemid 46026305)
28. Linz, S., Radtke, A. and von Haeseler, A. (2007) A maximum likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol., 24, 1312-1319. (Pubitemid 47343935)
29. Than, C. and Nakhleh, L. (2008) SPR-based tree reconciliation: non-binary trees and multiple solutions. In Proceedings of the 6th Asia Pacific Bioinformatics Conference. Kyoto, Japan, pp. 251-260.
30. Denamur, E., Lecointre, G., Darlu, P., Tenaillon, O., Acquaviva, C., Sayada, C., Sunjevaric, I., Rothstein, R., Elion, J., Taddei, F. et al. (2000) Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell., 103, 711-721.
31. Makarenkov, V., Boc, A., Delwiche, C.F., Diallo, A.B. and Philippe, H. (2006) New efficient algorithm for modeling partial and complete gene transfer scenarios. In Batagelj, V., Bock, H.H., Ferligoj, A. and Ziberna, A. (eds), Data Science and Classification. Springer, pp. 341-349.
32. Ray, S.C. (1998) SimPlot for Windows (version 1.6). Berlin, Germany, Baltimore, Md.
33. Archibald, J.M. and Roger, A.J. (2002) Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol., 316, 1041-105.
34. Paraskevis, D., Deforche, K., Lemey, K., Magiorkinis., Hatzakis, A. and Vandamme, A.M. (2005) SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics, 21, 1274-1275. (Pubitemid 40467958)
35. Lee, W.H. and Sung, W.K. (2008) RB-finder: an improved distance-based sliding window method to detect recombination breakpoints. J. Comput. Biol., 15, 881-898.
36. Martin, D.P., Lemey, P., Lott, M., Moulton, V., Posada, D. and Lefeuvre, P. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26, 2462-2463.
37. Delwiche, C.F. and Palmer, J.D. (1996) Rampant horizontal transfer and duplication of Rubisco genes in Eubacteria and Plastids. Mol. Biol. Evol., 13, 873-882. (Pubitemid 26240091)
38. Acinas, S.G., Marcelino, L.A., Klepac-Ceraj, V. and Polz, M.F. (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol., 38, 2629-2635. (Pubitemid 38525916)
39. Guindon, S. and Gascuel, O. (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704. (Pubitemid 37365050)
40. Robinson, D.R. and Foulds, L.R. (1981) Comparison of phylogenetic trees. Math. Biosciences, 53, 131-147. (Pubitemid 11129084)
41. Smith, J.M., Feil, E.J. and Smith, N.H. (2000) Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays, 22, 1115-1122. (Pubitemid 32010521)
42. Kuhner, M. and Felsenstein, J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol., 11, 459-468.
43. Guindon, S. and Gascuel, O. (2002) Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol., 19, 534-543. (Pubitemid 34289429)
44. Rambaut, A. and Grassly, N.C. (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13, 235-238. (Pubitemid 27249927)
45. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci., 8, 275-282.
46. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2009) GenBank. Nucleic Acids Res., 37, D26-D31.
47. Farris, J.S., Kallersjo, M., Kluge, A.G. and Bult, C. (1994) Testing significance of incongruence. Cladistics, 10, 3, 315-319.
48. Hasegawa, M., Hirohisa, K. and Taka-aki, Y. (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174. (Pubitemid 16227864)
49. Makarenkov, V. (2001) T-Rex: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics, 17, 664-668. (Pubitemid 32707593)
50. Vulic, M., Dionisio, F., Taddei, F. and Radman, M. (1997) Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl Acad. Sci. USA, 94, 9763-9767. (Pubitemid 27408137)