A distance-based method for detecting horizontal gene transfer in whole genomes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4983 LNBI, Issue , 2008, Pages 26-37

  Wei, Xintao ^a   Cowen, Lenore ^a   Brodley, Carla ^a   Brady, Arthur ^a   Sculley, D ^a   Slonim, Donna K ^a,b  

^a Tufts University   (United States)

^b TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATIONS.; DISTANCE METHOD; DISTANCE-BASED; GENOME EVOLUTION; HORIZONTAL GENE TRANSFER; HORIZONTAL TRANSFER; INTERNATIONAL SYMPOSIUM; PHYLOGENETIC TREE INFERENCE; SEQUENCED GENOMES;

BIOCOMMUNICATIONS; BIOINFORMATICS; DEMODULATION; GENE TRANSFER; INFORMATION SCIENCE;

TREES (MATHEMATICS);

EID: 49949112785     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-79450-9_4     Document Type: Conference Paper

References (32)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic. Acids. Res. 25(17), 3389-3402 (1997)
2. Anderson, F.E., Swofford, D.L.: Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol Phylogenet Evol. 33(2), 440-451 (2004)
3. Charbit, A., Autret, N.: Horizontal transfer of chromosomal DNA between the marine bacterium Vibrio furnissii and Escherichia coli revealed by sequence analysis. Microb. Comp. Genomics 3(2), 119-132 (1998)
4. Coenye, T., Vandamme, P.: Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes. FEMS Microbiol. Lett. 242(1), 117-126 (2005)
5. Davies, J.: Origins and evolution of antibiotic resistance. Microbiologia 12(1), 9-16 (1996)
6. Doolittle, W.F.: You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14(8), 307-311 (1998)
7. Doolittle, W.F.: Lateral genomics. Trends. Cell. Biol. 9(12), 5-8 (1999)
8. Eisen, J.A.: Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10(6), 606-611 (2000)
9. Felsenstein, J.: PHYLIP (Phylogeny Inference Package), version 3.66. Department of Genetics, University of Washington, Seattle, Washington (2002)
10. Hotopp, J.C., Clark, M.E., Oliveira, D.C., Foster, J.M., Fischer, P., Torres, M.C., Giebel, J.D., Kumar, N., Ishmael, N., Wang, S., et al.: Widespread lateral gene transfer from intra-cellular bacteria to multicellular eukaryotes. Widespread lateral gene transfer from intra-cellular bacteria to multicellular eukaryotes 317(5845), 1753-1756 (2007)
11. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al.: Initial sequencing and analysis of the human genome. Nature 409(6822), 860-921 (2001)
12. Lawrence, J.G., Ochman, H.: Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44(4), 383-397 (1997)
13. Lerat, E., Daubin, V., Moran, N.A.: From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol. 1(1), 19 (2003)
14. Ly, A., Henderson, J., Lu, A., Culham, D.E., Wood, J.M.: Osmoregulatory systems of Escherichia coli: identification of betaine-carnitine-choline transporter family member BetU and distributions of betU and trkG among pathogenic and nonpathogenic isolates. J. Bacteriol. 186(2), 296-306 (2004)
15. Martin, W.: Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21(2), 99-104 (1999)
16. Moya, A., Latorre, A., Sabater-Munoz, B., Silva, F.J.: Comparative molecular evolution of primary (Buchnera) and secondary symbionts of aphids based on two protein-coding genes. J. Mol. Evol. 55(2), 127-137 (2002)
17. Mrazek, J., Karlin, S.: Detecting alien genes in bacterial genomes. Ann. N. Y. Acad. Sci. 870, 314-329 (1999)
18. Planet, P.J.: Tree disagreement: measuring and testing incongruence in phylogenies. J. Biomed. Inform. 39(1), 86-102 (2006)
19. Podell, S., Gaasterland, T.: DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol 8(2), 16 (2007)
20. Poptsova, M.S., Gogarten, J.P.: The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol. Biol. 7, 45 (2007)
21. Remm, M., Storm, CE., Sonnhammer, E.L.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314(5), 1041-1052 (2001)
22. Ren, C.P., Beatson, S.A., Parkhill, J., Pallen, M.J.: The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli. J. Bacteriol. 187(4), 1430-1440 (2005)
23. Robinson, D.: Comparison of phylogenetic trees. Mathematical Biosciences 53, 131-147 (1981)
24. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4), 406-425 (1987)
25. Salzberg, S.L., White, O., Peterson, J., Eisen, J.A.: Microbial genes in the human genome: lateral transfer or gene loss? Science 292(5523), 1903-1906 (2001)
26. Schaffer, A.A., Aravind, L., Madden, T.L., Shavirin, S., Spouge, J.L., Wolf, Y.I., Koonin, E.V., Altschul, S.F.: Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic. Acids. Res. 29(14), 2994-3005 (2001)
27. Shimodaira, H.: An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51(3), 492-508 (2002)
28. Spaulding, A.W., von Dohlen, CD.: Phylogenetic characterization and molecular evolution of bacterial endosymbionts in psyllids (Hemiptera: Sternorrhyncha). Mol. Biol. Evol. 15(11), 1506-1513 (1998)
29. Sprenger, G.A.: Two open reading frames adjacent to the Escherichia coli K-12 tran-sketolase (tkt) gene show high similarity to the mannitol phosphotransferase system en-zymes from Escherichia coli and various gram-positive bacteria. Biochim. Biophys. Acta. 1158(1), 103-106 (1993)
30. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic. Acids. Res. 22(22), 4673-4680 (1994)
31. van Ham, R.C., Moya, A., Latorre, A.: Putative evolutionary origin of plasmids carrying the genes involved in leucine biosynthesis in Buchnera aphidicola (endosymbiont of aphids). J. Bacteriol. 179(15), 4768-4777 (1997)
32. Warwick, S.I., Legere, A., Simard, M.J., James, T.: Do escaped transgenes persist in nature? The case of an herbicide resistance transgene in a weedy Brassica rapa population. Mol. Ecol. (2007)