DarkHorse: A method for genome-wide prediction of horizontal gene transfer

Genome Biology

Volumn 8, Issue 2, 2007, Pages

  Podell, Sheila ^a   Gaasterland, Terry ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BACTERIAL GENETICS; CONTROLLED STUDY; ESCHERICHIA COLI; EUKARYOTE; GENE SEQUENCE; GENE TRANSFER; GENETIC ALGORITHM; GENETIC IDENTIFICATION; GENOME ANALYSIS; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; QUANTITATIVE ANALYSIS; RELIABILITY; REPRODUCIBILITY; ALGORITHM; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; HORIZONTAL GENE TRANSFER; METHODOLOGY; PROBABILITY;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE TRANSFER, HORIZONTAL; GENOMICS; PHYLOGENY; PROBABILITY; SOFTWARE;

EID: 34447513240     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-2-r16     Document Type: Article

References (49)

1. Koonin EV Makarova KS Aravind L Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55:709-742. 10.1146/annurev.micro.55.1.709 11544372
2. Lawrence JG Ochman H Reconciling the many faces of lateral gene transfer. Trends Microbiol 2002, 10:1-4. 10.1016/S0966-842X(01)02282-X 11755071
3. Andersson JO Lateral gene transfer in eukaryotes. Cell Mol Life Sci 2005, 62:1182-1197. 10.1007/s00018-005-4539-z 15761667
4. Gogarten JP Townsend JP Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 2005, 3:679-687. 10.1038/nrmicro1204 16138096
5. Bapteste E Susko E Leigh J MacLeod D Charlebois RL Doolittle WF Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 2005, 5:33. 1156881 15913459 10.1186/1471-2148-5-33
6. Embley TM Martin W Eukaryotic evolution, changes and challenges. Nature 2006, 440:623-630. 10.1038/nature04546 16572163
7. Ochman H Lerat E Daubin V Examining bacterial species under the specter of gene transfer and exchange. Proc Natl Acad Sci USA 2005, 102(Suppl 1):6595-6599. 1131874 15851673 10.1073/pnas.0502035102
8. Gevers D Cohan FM Lawrence JG Spratt BG Coenye T Feil EJ Stackebrandt E Van de Peer Y Vandamme P Thompson FL Swings J Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 2005, 3:733-739. 10.1038/ nrmicro1236 16138101
9. Ge F Wang LS Kim J The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 2005, 3:e316. 1233574 16122348 10.1371/journal.pbio.0030316
10. Gophna U Charlebois RL Doolittle WF Have archaeal genes contributed to bacterial virulence? Trends Microbiol 2004, 12:213-219. 10.1016/ j.tim.2004.03.002 15120140
11. Faguy DM Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease. BMC Infect Dis 2003, 3:13. 184401 12816550 10.1186/1471-2334-3-13
12. Ragan MA Harlow TJ Beiko RG Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol 2006, 14:4-8. 10.1016/j.tim.2005.11.004 16356716
13. Sharp PM Li WH The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-1295. 340524 3547335 10.1093/nar/15.3.1281
14. Lawrence JG Ochman H Amelioration of bacterial genomes: Rates of change and exchange. J Mol Evol 1997, 44:383-397. 10.1007/PL00006158 9089078
15. Garcia-Vallve S Guzman E Montero MA Romeu A HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 2003, 31:187-189. 165451 12519978 10.1093/nar/gkg004
16. Dalevi D Dubhashi D Hermansson M Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures. Bioinformatics 2006, 22:517-522. 10.1093/bioinformatics/btk029 16403797
17. Waack S Keller O Asper R Brodag T Damm C Fricke WF Surovcik K Meinicke P Merkl R Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7:142. 1489950 16542435 10.1186/1471-2105-7-142
18. Saunders NJ Boonmee P Peden JF Jarvis SA Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori BMC Genomics 2005, 6:9. 549213 15676066 10.1186/ 1471-2164-6-9
19. Tsirigos A Rigoutsos I A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res 2005, 33:3699-3707. 1174904 16006619 10.1093/nar/gki660
20. Koski LB Morton RA Golding GB Codon bias and base composition are poor indicators of horizontally transferred genes. Mol Biol Evol 2001, 18:404-412. 11230541
21. Wang B Limitations of compositional approach to identifying horizontally transferred genes. J Mol Evol 2001, 53:244-250. 10.1007/s002390010214 11523011
22. Gophna U Charlebois RL Doolittle WF Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus Trends Microbiol 2006, 14:64-69. 10.1016/j.tim.2005.12.008 16413191
23. Ortutay C Gaspari Z Toth G Jager E Vida G Orosz L Vellai T Speciation in Chlamydia: Genomewide phylogenetic analyses identified a reliable set of acquired genes. J Mol Evol 2003, 57:672-680. 10.1007/s00239-003-2517-3 14745536
24. Guindon S Perriere G Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol Biol Evol 2001, 18:1838-1840. 11504864
25. Tsirigos A Rigoutsos I A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res 2005, 33:922-933. 549390 15716310 10.1093/nar/gki187
26. Martin W Gene transfer from organelles to the nucleus: Frequent and in big chunks. Proc Natl Acad Sci USA 2003, 100:8612-8614. 166356 12861078 10.1073/pnas.1633606100
27. Santos SR Ochman H Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 2004, 6:754-759. 10.1111/j.1462-2920.2004.00617.x 15186354
28. Clarke GD Beiko RG Ragan MA Charlebois RL Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 2002, 184:2072-2080. 134965 11914337 10.1128/JB.184.8.2072-2080.2002
29. Lyubetsky VA V'Yugin VV Methods of horizontal gene transfer determination using phylogenetic data. In Silico Biol 2003, 3:17-31. 12762843
30. MacLeod D Charlebois RL Doolittle F Bapteste E Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol 2005, 5:27. 1087482 15819979 10.1186/1471-2148-5-27
31. Zhaxybayeva O Gogarten JP An improved probability mapping approach to assess genome mosaicism. BMC Genomics 2003, 4:37. 222983 12974984 10.1186/1471-2164-4-37
32. Daubin V Ochman H Quartet mapping and the extent of lateral transfer in bacterial genomes. Mol Biol Evol 2004, 21:86-89. 10.1093/molbev/msg234 12949130
33. Sicheritz-Ponten T Andersson SG A phylogenomic approach to microbial evolution. Nucleic Acids Res 2001, 29:545-552. 29656 11139625 10.1093/ nar/29.2.545
34. Frickey T Lupas AN PhyloGenie: Automated phylome generation and analysis. Nucleic Acids Res 2004, 32:5231-5238. 521674 15459293 10.1093/ nar/gkh867
35. Huang J Mullapudi N Sicheritz-Ponten T Kissinger JC A first glimpse into the pattern and scale of gene transfer in Apicomplexa Int J Parasitol 2004, 34:265-274. 10.1016/j.ijpara.2003.11.025 15003488
36. Koski LB Golding GB The closest BLAST hit is often not the nearest neighbor. J Mol Evol 2001, 52:540-542. 11443357
37. Eisen JA Horizontal gene transfer among microbial genomes: New insights from genome analysis. Curr Opin Genet Dev 2000, 10:606-611. 10.1016/ S0959-437X(00)00143-X 11088009
38. Pariasca JAT Sunaga A Miyazaki T Hisaka H Sonoda M Nakagawa H Sato T Cloning of cDNAs encoding senescence-associated genes, ACC synthase and ACC oxidase from stored snow pea pods (Pisum sativum L. var saccharatum) and their expression during pod storage. Postharvest Biol Technol 2001, 22:191-290. 10.1016/S0925-5214(01)00094-1
39. Ruepp A Graml W Santos-Martinez ML Koretke KK Volker C Mewes HW Frishman D Stocker S Lupas AN Baumeister W The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum Nature 2000, 407:508-513. 10.1038/35035069 11029001
40. Mongodin EF Hance IR Deboy RT Gill SR Daugherty S Huber R Fraser CM Stetter K Nelson KE Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species. J Bacteriol 2005, 187:4935-4944. 1169497 15995209 10.1128/JB.187.14.4935-4944.2005
41. Nelson KE Clayton RA Gill SR Gwinn ML Dodson RJ Haft DH Hickey EK Peterson JD Nelson WC Ketchum KA Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima Nature 1999, 399:323-329. 10.1038/20601 10360571
42. Nesbo CL L'Haridon S Stetter KO Doolittle WF Phylogenetic analyses of two 'archaeal' genes in thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol 2001, 18:362-375. 11230537
43. Loftus B Anderson I Davies R Alsmark UC Samuelson J Amedeo P Roncaglia P Berriman M Hirt RP Mann BJ The genome of the protist parasite Entamoeba histolytica Nature 2005, 433:865-868. 10.1038/nature03291 15729342
44. Sharma A Sojar HT Glurich I Honma K Kuramitsu HK Genco RJ Cloning, expression, and sequencing of a cell surface antigen containing a leucine-rich repeat motif from Bacteroides forsythus ATCC 43037. Infect Immun 1998, 66:5703-5710. 108721 9826345
45. NCBI GenBank Genomes ftp://ftp.ncbi.nih.gov/genbank/genomes/
46. dictyBase http://dictybase.org/db/cgi-bin/dictyBase/download/ blast_databases.pl
47. The TIGR Arabidopsis thaliana Database http://www.tigr.org/tdb/e2k1/ath1/
48. NCBI BLAST Database ftp://ftp.ncbi.nih.gov/blast/db/
49. NCBI Taxonomy Database ftp://ftp.ncbi.nih.gov/pub/taxonomy