Hostname: page-component-cd9895bd7-jn8rn Total loading time: 0 Render date: 2024-12-27T02:24:23.025Z Has data issue: false hasContentIssue false

Risks from GMOs due to Horizontal Gene Transfer

Published online by Cambridge University Press:  20 September 2008

Paul Keese*
Affiliation:
Office of the Gene Technology Regulator, PO Box 100 Woden, ACT 2606, Australia

Abstract

Core share and HTML view are not available for this content. However, as you have access to this content, a full PDF is available via the ‘Save PDF’ action button.

Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.

Type
Review Article
Copyright
© ISBR, EDP Sciences, 2008

References

Aaziz R, Tepfer M (1999) Recombination in RNA viruses and in virus-resistant transgenic plants. J. Gen. Virol. 80: 1339–1346
Abbot P, Aviles AE, Eller L, Durden LA (2007) Mixed infections, cryptic diversity, and vector-borne pathogens: evidence from Polygenis fleas and Bartonella species. Appl. Environ. Microbiol. 73: 6045–6052
Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186: 2629–2635 CrossRef
Adair TL, Kearney CM (2000) Recombination between a 3-kilobase tobacco mosaic virus transgene and a homologous viral construct in the restoration of viral and nonviral genes. Arch. Virol. 145: 1867–1883
Aeschbacher K, Messikommer R, Meile L, Wenk C (2005) Bt176 corn in poultry nutrition: physiological characteristics and fate of recombinant plant DNA in chickens. Poult. Sci. 84: 385–394
Agranovsky AA, Boyko VP, Karasev AV, Koonin EV, Dolja VV (1991) Putative 65 kDa protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins. J. Mol. Biol. 217: 603–610
Ambur OH, Frye SA, Tønjum T (2007) New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators. J. Bacteriol. 189: 2077–2085 CrossRef
Andersson JO (2005) Lateral gene transfer in eukaryotes. Cell Mol. Life Sci. 62: 1182–1197
Andersson JO, Sjögren AM, Horner DS, Murphy CA, Dyal PL, Svärd SG, Logsdon JM Jr, Ragan MA, Hirt RP, Roger AJ (2007) A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8: 51 CrossRef
Aoki S, Syōno K (1999) Horizontal gene transfer and mutation: Ngrol genes in the genome of Nicotiana glauca. Proc. Natl. Acad. Sci. USA 96: 13229–13234
Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14: 442–444 CrossRef
Ashby MK, Warry A, Bejarano ER, Khashoggi A, Burrell M, Lichtenstein CP (1997) Analysis of multiple copies of geminiviral DNA in the genome of four closely related Nicotiana species suggest a unique integration event. Plant Mol. Biol. 35: 313–321
Audic S, Robert C, Campagna B, Parinello H, Claverie JM, Raoult D, Drancourt M (2007) Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PLoS Genet. 3: e138
Babić A, Lindner AB, Vulić M, Stewart EJ, Radman M (2008) Direct visualization of horizontal gene transfer. Science 319: 1533–1536
Banner LM, Lai MMC (1991) Random nature of coronavirus RNA recombination in the absence of selection pressure. Virology 185: 441–445
Bateson MF, Lines RE, Revill P, Chaleeprom W, Ha CV, Gibbs AJ, Dale JL (2002) On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus. J. Gen. Virol. 83: 2575–2585
Bathe S, Mohan TV, Wuertz S, Hausner M (2004) Bioaugmentation of a sequencing batch biofilm reactor by horizontal gene transfer. Water Sci. Technol. 49: 337–344
Beaber JW, Hochhut B, Waldor MK (2004) SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427: 72–74 CrossRef
Beagle JM, Apgar GA, Jones KL, Griswold KE, Radcliffe JS, Qiu X, Lightfoot DA, Iqbal MJ (2006) The digestive fate of Escherichia coli glutamate dehydrogenase deoxyribonucleic acid from transgenic corn in diets fed to weanling pigs. J. Anim Sci. 84: 597–607
Becker Y (2000) Evolution of viruses by acquisition of cellular RNA or DNA nucleotide sequences and genes: An introduction. Virus Genes 21: 7–12 CrossRef
Beiko, RG, Harlow, TJ, Ragan, MA (2005) Highways of gene sharing in prokaryotes. Proc. Natl. Acad. Sci. USA 102: 1433214337 CrossRef
Bejarano ER, Khashoggi A, Witty M, Lichtenstein C (1996) Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution. Proc. Natl. Acad. Sci. USA 93: 759–764 CrossRef
Belfort M, Berbyshire V, Parker MM, Cousineau B, Lambowitz AM (2002) Mobile introns: Pathways and proteins. In Craig NL, Craigie R, Gellert M, Lambowitz AM, eds, Mobile DNA II, American Society for Microbiology, pp 761–783
Bennett PM, Livesey CT, Nathwani D, Reeves DS, Saunders JR, Wise R (2004) An assessment of the risks associated with the use of antibiotic resistance genes in genetically modified plants: report of the Working Party of the British Society for Antimicrobial Chemotherapy. J. Antimicrob. Chemother. 53: 418–431
Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141–147
Bird DM, Koltai H (2000) Plant parasitic nematodes: habitats, hormones, and horizontally-acquired genes. J. Plant Growth Reg. 19: 183–194
Böhne, A, Brunet, F, Galiana-Arnoux, D, Schultheis, C, Volff, JN (2008) Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Res. 16: 203215 CrossRef
Bonnet J, Fraile A, Sacristán S, Malpica JM, García-Arenal F (2005) Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus. Virology 332: 359–368
Borja M, Rubio T, Scholthof HB, Jackson AO (1999) Restoration of wild-type virus by double recombination of tombusvirus mutants with a host transgene. Mol. Plant. Microbe Interact. 12: 153–162 CrossRef
Bos L (1999) Plant viruses, unique and intriguing plant pathogens – a textbook of plant virology. Backhuys Publishers, Leiden, The Netherlands
Botstein D (1980) A theory of modular evolution for bacteriophages. Ann. NY Acad. Sci. 354: 484–490
Boucher Y, Labbate M, Koenig JE, Stokes HW (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol. 15: 301–309 CrossRef
Boyle DB, Coupar BE, Gibbs AJ, Seigman LJ, Both GW (1987) Fowlpox virus thymidine kinase: nucleotide sequence and relationships to other thymidine kinases. Virology 156: 355–365 CrossRef
Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13: 278–284
Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC (1998) Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J. 17: 6739–6746 CrossRef
Brinkmann N, Tebbe CC (2007) Leaf-feeding larvae of Manduca sexta (Insecta, Lepidoptera) drastically reduce copy numbers of aadA antibiotic resistance genes from transplastomic tobacco but maintain intact aadA genes in their feces. Environ. Biosafety. Res. 6: 121–133
Bromham L, Penny D (2003) The modern molecular clock. Nature Rev. Genet. 4: 216–224
Broothaerts W, Mitchell HJ, Weir B, Kaines S, Smith LM, Yang W, Mayer JE, Roa-Rodriguez C, Jefferson RA (2005) Gene transfer to plants by diverse species of bacteria. Nature 433: 629–633 CrossRef
Bruyère A, Wantroba M, Flasinski S, Dzianott A, Bujarski JJ (2000) Frequent homologous recombination events between molecules of one RNA component in a multipartite RNA virus. J. Virol. 74: 4214–4219
Bujarski JJ, Nagy PD (1996) Different mechanisms of homologous and nonhomologous recombination in brome mosaic virus: Role of RNA sequences and replicase proteins. Sem. Virol. 7: 363–372
Bundock P, Den DRA, Beijersbergen A, Hooykaas PJJ (1995) Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae. EMBO J. 14: 3206–3214
Burrus V, Waldor MK (2004) Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 155: 376–386
Bushman F (2002) Lateral DNA transfer: mechanisms and consequences. Cold Spring Harbor Laboratory Press, New York, USA
Canbäck B, Tamas I, Andersson SG (2004) A phylogenomic study of endosymbiotic bacteria. Mol. Biol. Evol. 21: 1110–1122
Carattoli A (2001) Importance of integrons in the diffusion of resistance. Vet. Res. 32: 243–259
Carrère I, Tepfer M, Jacquemond M (1999) Recombinants of cucumber mosaic virus (CMV): Determinants of host range and symptomatology. Arch. Virol. 144: 365–379
Cascales E, Christie PJ (2004) Definition of a bacterial type IV secretion pathway for a DNA substrate. Science 304: 1170–1173 CrossRef
Chambers PA, Duggan PS, Heritage J, Forbes JM (2002) The fate of antibiotic resistance marker genes in transgenic plant feed material fed to chickens. J. Antimicrob. Chemother. 49: 161–164
Chare ER, Gould EA, Holmes EC (2003) Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. J. Gen. Virol. 84: 2691–2703
Chen I, Christie PJ, Dubnau D (2005) The ins and outs of DNA transfer in bacteria. Science 310: 1456–1460 CrossRef
Chowdhury EH, Kuribara H, Hino A, Sultana P, Mikami O, Shimada N, Guruge KS, Saito M, Nakajima Y (2003) Detection of corn intrinsic and recombinant DNA fragments and Cry1Ab protein in the gastrointestinal contents of pigs fed genetically modified corn Bt11. J. Anim Sci. 81: 2546–2551
Chowdhury EH, Mikami O, Murata H, Sultana P, Shimada N, Yoshioka M, Guruge KS, Yamamoto S, Miyazaki S, Yamanaka N, Nakajima Y (2004) Fate of maize intrinsic and recombinant genes in calves fed genetically modified maize Bt11. J. Food Prot. 67: 365–370
Cummins J, Ho MW, Ryan A (2000) Hazardous CaMV promoter? Nat. Biotechnol. 18: 363–363
d'Adda di Fagagna F, Weller GR, Doherty AJ, Jackson SP (2003) The Gam protein of bacteriophage Mu is an orthologue of eukaryotic Ku. EMBO Rep. 4: 47–52
D'Costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling the antibiotic resistome. Science 311: 374–377
Daubin V, Ochman H (2004) Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14: 1036–1042
Daubin V, Perrière G (2003) G+C3 structuring along the genome: a common feature in prokaryotes. Mol. Biol. Evol. 20: 471–483
Davison J (1999) Genetic exchange between bacteria in the environment. Plasmid 42: 73–91 CrossRef
de Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nature Biotech. 16: 839–842
de la Cruz F, Davies J (2000) Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol. 8: 128–133
De Vries J, Wackernagel W (1998) Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker-rescue transformation. Mol. Gen. Genet. 257: 606–613
De Vries J, Wackernagel W (2002) Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc. Natl. Acad. Sci. USA 99: 2094–2099
De Vries J, Meier P, Wackernagel W (2001) The natural transformation of the soil bacteria Pseudomonas stutzeri and Acinetobacter sp. by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. FEMS Microbiol. Lett. 195: 211–215
Deaville ER, Maddison BC (2005) Detection of transgenic and endogenous plant DNA fragments in the blood, tissues, and digesta of broilers. J. Agric. Food Chem. 53: 10268–10275
Deitsch K, Driskill C, Wellems T (2001) Transformation of malaria parasites by the spontaneous uptake and expression of DNA from human erythrocytes. Nucleic Acids Res. 29: 850–853 CrossRef
Demanèche S, Bertolla F, Buret F, Nalin R, Sailland A, Auriol P, Vogel TM, Simonet P (2001) Laboratory-scale evidence for lightning-mediated gene transfer in soil. Appl. Environ. Microbiol. 67: 3440–3444
DeMarco R, Mathieson W, Dillon GP, Wilson AR (2007) Schistosome albumin is of host, not parasite, origin. Int. J. Parasitol. 37: 1201–1208
Derbise A, Chenal-Francisque V, Pouillot F, Fayolle C, Prévost M-C, Médigue C, Hinnebusch BJ, Carniel E (2007) A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus. Mol. Microbiol. 63: 1145–1157
Ding SW, Shi BJ, Li WX, Symons RH (1996) An interspecies hybrid RNA virus is significantly more virulent than either parental virus. Proc. Natl. Acad. Sci. USA 93: 7470–7474
Ding Z, Atmakuri K, Christie PJ (2003) The outs and ins of bacterial type IV secretion substrates. Trends Microbiol. 11: 527–535
Doolittle RF, Feng DF, Anderson KL, Alberro MR (1990) A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J. Mol. Evol. 31: 383–388
Doolittle WF (1998) You are what you eat: A gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14: 307–311 CrossRef
Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601–603 CrossRef
Dorward DW, Garon CF, Judd RC (1989) Export and intercellular transfer of DNA via membrane blebs of Neisseria gonorrhoeae. J. Bacteriol. 171: 2499–2505
Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG (2001) The highly reduced genome of an enslaved algal nucleus. Nature 410: 1091–1096 CrossRef
Douville M, Gagné F, Blaise C, André C (2007) Occurrence and persistence of Bacillus thuringiensis (Bt) and transgenic Bt corn cry1Ab gene from an aquatic environment. Ecotoxicol. Environ. Saf. 66: 195–203
Doyle M, Fookes M, Mangan MW, Wain J, Dorman CJ (2007) An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315: 251–252 CrossRef
Draghi JA, Turner PE (2006) DNA secretion and gene-level selection in bacteria. Microbiology 152: 2683–2688 CrossRef
Dreiseikelmann B (1994) Translocation of DNA across bacterial membranes. Microbiol. Rev. 58: 293–316
Dubnau D (1999) DNA uptake in bacteria. Annu. Rev. Microbiol. 53: 217–244 CrossRef
Dufraigne C, Fertil B, Lespinats S, Giron A, Deschavanne P (2005) Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res. 33: e6
Duggan PS, Chambers PA, Heritage J, Michael FJ (2003) Fate of genetically modified maize DNA in the oral cavity and rumen of sheep. Br. J. Nutr. 89: 159–166
Dykhuizen DE, Baranton G (2001) The implications of a low rate of horizontal transfer in Borrelia. Trends Microbiol. 9: 344–350 CrossRef
Einspanier R, Klotz A, Kraft J, Aulrich K, Poser R, Schwägele F, Jahreis G, Flachowsky G (2001) The fate of forage plant DNA in animals: a collaborative case-study investigating cattle and chicken fed recombinant plant material. European Food Res. Tech. 212: 129–139
Eisen JA (2000) Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10: 606–611
Escobar-Páramo P, Sabbagh A, Darlu P, Pradillon O, Vaury C, Denamur E, Lecointre G (2004) Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study. Mol. Phylogenet. Evol. 30: 243–250
Espinosa-Urgel M (2004) Plant-associated Pseudomonas populations: molecular biology, DNA dynamics, and gene transfer. Plasmid 52: 139–150 CrossRef
Falk BW, Bruening G (1994) Will transgenic crops generate new viruses and new diseases? Science 263: 1395–1396
Fernandez-Cuartero B, Burgyan J, Aranda MA, Salanki K, Moriones E, Garcia-Arenal F (1994) Increase in the relative fitness of a plant virus RNA associated with its recombinant nature. Virology 203: 373–377
Feschotte C, Zhang X, Wessler SR (2002) Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. In Craig NL, Craigie R, Gellert M, Lambowitz AM, eds, Mobile DNA II, American Society for Microbiology, pp 1147–1158
Filée J, Forterre P, Sen-Lin T, Laurent J (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J. Mol. Evol. 54: 763–773
Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315: 476–480
Friesen TL, Stuckenbrock EH, Liu Z, Meinhardt S, Ling H, Faris JD, Rasmussen JB, Solomon PS, McDonald BA, Oliver RP (2006) Emergence of a new disease as a result of interspecific virulence gene transfer. Nature Genet. 38: 953–956
Frischmuth T, Stanley J (1998) Recombination between viral DNA and the transgenic coat protein gene of African cassava mosaic geminivirus. J. Gen. Virol. 79: 1265–1271
Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y (2005) Recombination every day: Abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol. 3: 389–395 CrossRef
Fu, M, Deng, R, Wang, J, Wang, X (2008) Detection and analysis of horizontal gene transfer in herpesvirus. Virus Res. 131: 6576 CrossRef
Gal S, Pisan B, Hohn T, Grimsley N, Hohn B (1992) Agroinfection of transgenic plants leads to viable cauliflower mosaic virus by intermolecular recombination. Virology 187: 525–533 CrossRef
Garcia-Vallve S, Guzman E, Montero MA, Romeu A (2003) HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31: 187–189
Gebhard F, Smalla K (1998) Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA. Appl. Environ. Microbiol. 64: 1550–1554
Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the “gene-jockeying” tool. Microbiol. Mol. Biol. Rev. 67: 16–37
Gibbs A (1987) Molecular evolution of viruses; “trees”, “clocks” and “modules”. J. Cell Sci. Suppl. 7: 319–337
Gibbs MJ, Weiller GF (1999) Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus. Proc. Natl. Acad. Sci. USA 96: 8022–8027 CrossRef
Gibbs MJ, Armstrong JS, Gibbs AJ (2001) Recombination in the hemagglutinin gene of the 1918 “Spanish Flu”. Science 293: 1842–1845
Gladyshev, EA, Meselson, M, Arkhipova, IR (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320: 12101213 CrossRef
Gogarten JP, Olendzenski L (1999) Orthologs, paralogs and genome comparisons. Curr. Opin. Genet. Dev. 9: 630–636
Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19: 2226–2238
Gomis-Rüth FX, Solà M, de la Cruz F, Coll M (2004) Coupling factors in macromolecular type-IV secretion machineries. Curr. Pharmaceut. Design 10: 1551–1565
Gray MW (1993) Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3: 884–890
Greene AE, Allison RF (1994) Recombination between viral RNA and transgenic plant transcripts. Science 263: 1423–1425
Greene AE, Allison RF (1996) Deletions in the 3' untranslated region of cowpea chlorotic mottle virus transgene reduce recovery of recombinant viruses in transgenic plants. Virology 225: 231–234
Grillot-Courvalin C, Goussard S, Courvalin P (2002) Wild-type intracellular bacteria deliver DNA into mammalian cells. Cell. Microbiol. 4: 177–186
Grindley ND, Whiteson KL, Rice PA (2006) Mechanisms of site-specific recombination. Ann. Rev. Biochem. 75: 567–605 CrossRef
Grohmann E, Muth G, Espinosa M (2003) Conjugative plasmid transfer in gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67: 277–301
GTEC (Gene Technology Ethics Committee) (2006) Working paper: ethical issues arising from trans-species gene transfer. Available at http://www.ogtr.gov.au/ pdf/committee/trans-speciesGeneTransfer.pdf (accessed 17 April 2008)
Guindon S, Perrière G (2001) Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol. Biol. Evol. 18: 1838–1840
Guljamow A, Jenke-Kodama H, Saumweber H, Quillardet P, Frangeul L, Castets AM, Bouchier C, Tandeau de Marsac N, Dittmann E (2007) Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium. Curr. Biol. 17: R757–R759
Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogeny. Theor. Pop. Biol. 61: 423–434
Hacker J, Blum-Oehler G, Mühldorfer I, Tschäpe H (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23: 1089–1097
Hakenbeck R, Balmelle N, Weber B, Gardes C, Keck W, De Saizieu A (2001) Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69: 2477–2486
Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Euk. Cell 4: 1102–1115
Hao W, Golding GB (2004) Patterns of bacterial gene movement. Mol. Biol. Evol. 21: 1294–1307
Harper G, Osuji JO, Heslop-Harrison JS, Hull R (1999) Integration of banana streak badnavirus into the Musa genome: Molecular and cytogenetic evidence. Virology 255: 207–213 CrossRef
Harper G, Hull R, Lockhart B, Olszewski N (2002) Viral sequences integrated into plant genomes. Ann. Rev. Phytopath. 40: 119–136 CrossRef
Haupt S, Oparka KJ, Sauer N, Neumann S (2001) Macromolecular trafficking between Nicotiana tabacum and the holoparasite Cuscuta reflexa. J. Exp. Bot. 52: 173–177
Heinemann JA, Sprague GF Jr (1989) Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340: 205–209
Hendrickx L, Hausner M, Wuertz S (2003) Natural genetic transformation in monoculture Acinetobacter sp. strain BD413 biofilms. Appl. Environ. Microbiol. 69: 1721–1727
Hendrix RW, Smith MCM, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage. Proc. Natl. Acad. Sci. USA 96: 2192–2197 CrossRef
Heuer H, Smalla K (2007) Horizontal gene transfer between bacteria. Environ. Biosafety. Res. 6: 3–13
Hijri M, Sanders IR (2005) Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei. Nature 433: 160–163 CrossRef
Hill RA (2005) Conceptualizing risk assessment methodology for genetically modified organisms. Environ. Biosafety Res. 4: 67–70 CrossRef
Ho MW, Ryan A, Cummins J (2000) Cauliflower mosaic viral promoter – a recipe for disaster? Microb. Ecol. Health Dis. 11: 194–197
Hofmann C, Sambade A, Heinlein M (2007) Plasmodesmata and intercellular transport of viral RNA. Biochem. Soc. Trans. 35: 142–145
Homma K, Fukuchi S, Nakamura Y, Gojobori T, Nishikawa K (2007) Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in eight species of γ-protobacteria. Mol. Biol. Evol. 24: 808–813
Hong SH, Kim TY, Lee SY (2004) Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl. Microbiol. Biotechnol. 65: 203–210
Hooper SD, Berg OG (2002) Detection of genes with atypical nucleotide sequence in microbial genomes. J. Mol. Evol. 54: 365–375
Hotopp JC, Clark ME, Oliveira DC, Foster JM, Fischer P, Torres MC, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317: 1753–1756
Houck MA, Clark JB, Peterson KR, Kidwell MG (1991) Possible horizontal transfer of Drosophila genes by the mite Proctolaelaps regalis. Science 253: 1125–1128
Huang J, Mullapudi N, Sicheritz-Ponten T, Kissinger JC (2004) A first glimpse into the pattern and scale of gene transfer in the Apicomplexa. Int. J. Parasitol. 34 : 265–274 CrossRef
Hughes AL, Friedman R (2003) Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses. Mol. Biol. Evol. 20: 979–987
Hughes AL, Friedman R (2005) Poxvirus genome evolution by gene gain and loss. Mol. Phylogenet. Evol. 35: 186–195
Hull R, Covey SN, Dale P (2000) Genetically modified plants and the 35S promoter: assessing the risks and enhancing the debate. Microb. Ecol. Health Dis. 12: 1–5
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921
Intrieri MC, Buiatti M (2001) The horizontal transfer of Agrobacterium rhizogenes genes and the evolution of the genus Nicotiana. Mol. Phylogenet. Evol. 20: 100–110
Jain R, Rivera MC, Moore JE, Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20: 1598–1602
Jakab G, Vaistij FE, Droz E, Malnoe P (1997) Transgenic plants expressing viral sequences create a favourable environment for recombination between viral sequences. In Tepfer M, Balázs E, eds, Virus-resistant transgenic plants: potential ecological impact, pp 45–51
Jennings JC, Albee LD, Kolwyck DC, Surber JB, Taylor ML, Hartnell GF, Lirette RP, Glenn KC (2003a) Attempts to detect transgenic and endogenous plant DNA and transgenic protein in muscle from broilers fed YieldGard Corn Borer Corn. Poult. Sci. 82: 371–380
Jennings JC, Kolwyck DC, Kays SB, Whetsell AJ, Surber JB, Cromwell GL, Lirette RP, Glenn KC (2003b) Determining whether transgenic and endogenous plant DNA and transgenic protein are detectable in muscle from swine fed Roundup Ready soybean meal. J. Anim Sci. 81: 1447–1455
Jiang SC, Paul JH (1998) Gene transfer by transduction in the marine environment. Appl. Environ. Microbiol. 64: 2780–2787
Johnson MD, Oldach D, Delwiche CF, Stoecker DK (2007) Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra. Nature 445: 426–428 CrossRef
Jones JG, Gardener S, Simon BM, Pickup RW (1986) Antibiotic resistant bacteria in Windermere and two remote upland tarns in the English Lake District. J. Appl. Bacteriol. 60: 443–453
Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19: 68–72
Kadurugamuwa, JL, Beveridge, TJ (1997) Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release. J. Antimicrob. Chemother. 40: 615621 CrossRef
Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, Mori H, Ikemura T (2001) Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 276: 89–99 CrossRef
Karlin S, Mrazek J, Campbell AM (1998) Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29: 1341–1355
Kazazian HH Jr (2004) Mobile elements: drivers of genome evolution. Science 303: 1626–1632 CrossRef
Keese, P, Symons, RH (1985) Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc. Natl. Acad. Sci. USA 82: 45824586 CrossRef
Kharazmi M, Bauer T, Hammes WP, Hertel C (2003) Effect of food processing on the fate of DNA with regard to degradation and transformation capability in Bacillus subtilis. Syst. Appl. Microbiol. 26: 495–501
Khatchikian, D, Orlich, M, Rott, R (1989) Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340: 156157 CrossRef
Kleter GA, Peijnenburg AA, Aarts HJ (2005) Health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops. J. Biomed. Biotechnol. 2005: 326–352
Knipe DM, Howley PM (2001) Fields Virology. Lippincott Williams & Wilkins, Philadelphia, USA
Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29: 3742–3756
Kohli A, Griffiths S, Palacios N, Twyman RM, Vain P, Laurie DA, Christou P (1999) Molecular characterization of transforming plasmid rearrangements in transgenic rice reveals a recombination hotspot in the CaMV 35S promoter and confirms the predominance of microhomology mediated recombination. Plant J. 17: 591–601 CrossRef
Koonin EV (2007) The Biological Big Bang model for the major transitions in evolution. Biol. Direct. 2: 21
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55: 709–742 CrossRef
Korbel JO, Snel B, Huynen MA, Bork P (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18: 158–162
Koski LB, Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52: 540–542
Koski LB, Morton RA, Golding GB (2001) Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18: 404–412
Kroll JS, Wilks KE, Farrant JL, Langford PR (1998) Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens. Proc. Natl. Acad. Sci. USA 95: 12381–12385
Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V (2001) Genetic transformation of HeLa cells by Agrobacterium. Proc. Natl. Acad. Sci. USA 98: 1871–1876
Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13: 1589–1594 CrossRef
Kurland CG (2005) What tangled web: barriers to rampant horizontal gene transfer. Bioessays 27: 741–747 CrossRef
Kurland CG, Canback B, Berg OG (2003) Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. USA 100: 9658–9662 CrossRef
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14: 169–181 CrossRef
Lambert KN, Allen KD, Sussex IM (1999) Cloning and characterization of an esophageal-gland-specific chorismate mutase from the phytoparasitic nematode Meloidogyne javanica. Mol. Plant-Microbe Interact. 12: 328–336
Lambowitz AM, Zimmerly S (2004) Mobile Group II Introns. Annu. Rev. Genet. 38: 1–35
Lang AS, Beatty JT (2001) The gene transfer agent of Rhodobacter capsulatus and “constitutive transduction” in prokaryotes. Arch. Microbiol. 175: 241–249
Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 9413–9417
Lawrence JG, Ochman H (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10: 1–4
Lebrun E, Santini JM, Brugna M, Ducluzeau AL, Ouchane S, Schoepp-Cothenet B, Baymann F, Nitschke W (2006) The rieske protein: A case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction. Mol. Biol. Evol. 23: 1180–1191
Legg JP, Thresh JM (2000) Cassava mosaic virus disease in East Africa: a dynamic disease in a changing environment. Virus Res. 71: 135–149 CrossRef
Li S, Nosenko T, Hackett JD, Bhattacharya D (2006) Phylogenomic analysis identifies red algal genes of endosymbiotic origin in the chromalveolates. Mol. Biol. Evol. 23: 663–674
Lilley AK, Bailey MJ, Barr M, Kilshaw K, Timms-Wilson TM, Day MJ, Norris SJ, Jones TH, Godfray HCJ (2003) Population dynamics and gene transfer in genetically modified bacteria in a model microcosm. Mol. Ecol. 12: 3097–3107
Lindbo JA, Dougherty WG (1992) Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 189: 725–733 CrossRef
Lorenz MG, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58: 563–602
Maeda S, Ito M, Ando T, Ishimoto Y, Fujisawa Y, Takahashi H, Matsuda A, Sawamura A, Kato S (2006) Horizontal transfer of nonconjugative plasmids in a colony biofilm of Escherichia coli. FEMS Microbiol. Lett. 255: 115–120
Majewski J (2001) Sexual isolation in bacteria. FEMS Microbiol. Lett. 199: 161–169
Majewski J, Cohan FM (1999) DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153: 1525–1533
Marri PR, Hao W, Golding GB (2007) The role of laterally transferred genes in adaptive evolution. BMC Evol. Biol. 7: 21
Marrs B (1974) Genetic recombination in Rhodopseudomonas capsulata. Proc. Natl. Acad. Sci. USA 71: 971–973 CrossRef
Martin W (2003) Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc. Natl. Acad. Sci. USA 100: 8612–8614 CrossRef
Masuta C, Kuwata S, Matzuzaki T, Takanami Y, Koiwai A (1992) A plant virus satellite RNA exhibits a significant sequence complementarity to a chloroplast tRNA. Nucl. Acids Res. 20: 2885
Matic I, Taddei F, Radman M (1996) Genetic barriers among bacteria. Trends Microbiol. 4: 69–72 CrossRef
Matsui K, Ishii N, Kawabata Z (2003) Release of extracellular transformable plasmid DNA from Escherichia coli cocultivated with algae. Appl. Environ. Microbiol. 69: 2399–2404
Mayo MA, Jolly CA (1991) The 5'-terminal sequence of potato leafroll virus RNA: evidence of recombination between virus and host RNA. J. Gen. Virol. 72: 2591–2595
Mazel D, Davies J (1999) Antibiotic resistance in microbes. Cell Mol. Life Sci. 56: 742–754
Mazza R, Soave M, Morlacchini M, Piva G, Marocco A (2005) Assessing the transfer of genetically modified DNA from feed to animal tissues. Transgenic Res. 14: 775–784
McClure MA (2000) The complexities of genome analysis, the Retroid agent perspective. Bioinformatics 16: 79–95
Meibom KL, Blokesch M, Dolganov NA, Wu CY, Schoolnik GK (2005) Chitin induces natural competence in Vibrio cholerae. Science 310: 1775–1777 CrossRef
Mel SF, Mekalanos JJ (1996) Modulation of horizontal gene transfer in pathogenic bacteria by in vivo signals. Cell 87: 795–798
Mercer DK, Scott KP, Bruce-Johnson WA, Glover LA, Flint HJ (1999) Fate of free DNA and transformation of the oral bacterium Streptococcus gordonii DL1 by plasmid DNA in human saliva. Appl. Environ. Microbiol. 65: 6–10
Meyers G, Tautz N, Dubovi EJ, Thiel HJ (1991) Viral cytopathogenicity correlated with integration of ubiquitin-coding sequences. Virology 180: 602–616
Michael CA, Gillings MR, Holmes AJ, Hughes L, Andrew NR, Holley MP, Stokes HW (2004) Mobile gene cassettes: a fundamental resource for bacterial evolution. Am. Nat. 164: 1–12
Mild M, Esbjörnsson J, Fenyö EM, Medstrand P (2007) Frequent intrapatient recombination between HIV-1 R5 and X4 envelopes: Implications for coreceptor switch. J. Virol. 81: 3369–3376
Mira A, Klasson L, Andersson SG (2002) Microbial genome evolution: sources of variability. Curr. Opin. Microbiol. 5: 506–512
Mohr KI, Tebbe CC (2007) Field study results on the probability and risk of a horizontal gene transfer from transgenic herbicide-resistant oilseed rape pollen to gut bacteria of bees. Appl. Microbiol. Biotechnol. 75: 573–582
Molin S, Tolker-Nielsen T (2003) Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr. Opin. Biotechnol. 14: 255–261
Moran JV, Gilbert N (2002) Mammalian LINE-1 retrotransposons and related elements. In Craig NL, Craigie R, Gellert M, Lambowitz AM, eds, Mobile DNA II, American Society for Microbiology, pp 836–869
Mower JP, Stefanovic S, Young GJ, Palmer JD (2004) Plant genetics: gene transfer from parasitic to host plants. Nature 432: 165–166 CrossRef
Nagy PD, Bujarski JJ (1996) Homologous RNA recombination in brome mosaic virus: AU-rich sequences decrease the accuracy of crossovers. J. Virol. 70: 415–426
Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36: 760–766
Nemeth A, Wurz A, Artim L, Charlton S, Dana G, Glenn K, Hunst P, Jennings J, Shilito R, Song P (2004) Sensitive PCR analysis of animal tissue samples for fragments of endogenous and transgenic plant DNA. J. Agric. Food Chem. 52: 6129–6135
Nesbø CL, L'Haridon S, Stetter KO, Doolittle WF (2001) Phylogenetic analyses of two “archaeal” genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol. Biol. Evol. 18: 362–375
Netherwood T, Martín-Orúe SM, O'Donnell AG, Gockling S, Graham J, Mathers JC, Gilbert HJ (2004) Assessing the survival of transgenic plant DNA in the human gastrointestinal tract. Nat. Biotechnol. 22: 204–209
Nielsen KM (1998) Barriers to horizontal gene transfer by natural transformation in soil bacteria. APMIS 106: 77–84
Nielsen KM, Townsend JP (2004) Monitoring and modeling horizontal gene transfer. Nature Biotech. 22: 1110–1114 CrossRef
Nielsen KM, van Elsas JD (2001) Stimulatory effects of compounds present in the rhizosphere on natural transformation of Acinetobacter sp. BD413 in soil. Soil Biol. Biochem. 33: 345–357
Nielsen, KM, Bones, AM, Smalla, K, van Elsas, JD (1998) Horizontal gene transfer from transgenic plants to terristrial bacteria – a rare event? FEMS Microbiol. Rev. 22: 79103 CrossRef
Nielsen, KM, van Elsas, JD, Smalla, K (2000a) Transformation of Acinetobacter sp. strain BD413 (pFGΔnptII) with transgenic plant DNA in soil microcosms and effects of kanamycin selection of transformants. Appl. Environ. Microbiol. 66: 12371242 CrossRef
Nielsen KM, Smalla K, van Elsas JD (2000b) Natural transformation of Acinetobacter sp. strain BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens, and Burkholderia cepacia in soil microcosms. Appl. Environ. Microbiol. 66: 206–212
Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D (2007) Release and persistence of extracellular DNA in the environment. Environ. Biosafety. Res. 6: 37–53
Nosenko T, Bhattacharya D (2007) Horizontal gene transfer in chromalveolates. BMC Evol. Biol. 7: 173
Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J. Bacteriol. 186: 6575–6585
Ochman H, Lawrence JG, Grolsman E (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304
OGTR (Office of the Gene Technology Regulator) (2007) Risk Analysis Framework, Australian Government, Canberra, ACT. Available at http://www.ogtr.gov.au/ pdf/public/raffinal3.pdf (accessed 17 April 2008)
Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ (2007) Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J. Gen. Virol. 88: 298–315
Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284: 604–607 CrossRef
Osborn AM, Böltner D (2002) When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Plasmid 48: 202–212
Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M (2004) Genetic analyses from ancient DNA. Annu. Rev. Genet. 38: 645–679
Pallen MJ, Wren BW (2007) Bacterial pathogenomics. Nature 449: 835–842
Parkinson J, Blaxter M (2003) SimiTri-visualizing similarity relationships for groups of sequences. Bioinformatics 19: 390–395
Pastwa E, Błasiak J (2007) Non-homologous DNA end joining. Acta Biochim. Pol. 50: 891–908
Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty, J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071–2074
Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, Knowles BB (2004) Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7: 597–606
Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR, Brucker W, Kumar V, Kandasamy J, Keenan L, Bardarov S, Kriako J, Lawrence JG, Jacobs WR Jr, Hendrix RW, Hatfull GF (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171–182
Perumbakkam S, Hess TF, Crawford RL (2006) A bioremediation approach using natural transformation in pure-culture and mixed-population biofilms. Biodegradation 17: 545–557 CrossRef
Peterson-Burch BD, Voytas DF (2002) Genes of the Pseudoviridae (Ty1/copia retrotransposons). Mol. Biol. Evol. 19: 1832–1845
Phale PS, Basu A, Majhi PD, Deveryshetty J, Vamsee-Krishna C, Shrivastava R (2007) Metabolic diversity in bacterial degradation of aromatic compounds. OMICS 11: 252–279 CrossRef
Phipps RH, Deaville ER, Maddison BC (2003) Detection of transgenic and endogenous plant DNA in rumen fluid, duodenal digesta, milk, blood, and feces of lactating dairy cows. J. Dairy Sci. 86: 4070–4078
Pierce SK, Massey SE, Hanten JJ, Curtis NE (2003) Horizontal transfer of functional nuclear genes between multicellular organisms. Biol. Bull. 204: 237–240
Piers KL, Heath JD, Liang X, Stephens KM, Nester EW (1996) Agrobacterium tumefaciens-mediated transformation of yeast. Proc. Natl. Acad. Sci. USA 93: 1613–1618
Pilhofer M, Bauer AP, Schrallhammer M, Richter L, Ludwig W, Schleifer KH, Petroni G (2007) Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method. Nucleic Acids Res. 35: e135
Piskurek O, Okada N (2007) Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc. Natl. Acad. Sci. USA 104: 12046–12051
Pita JS, Fondong VN, Sangare A, Otim-Nape GW, Ogwal S, Fauquet CM (2001) Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J. Gen. Virol. 82: 655–665
Pontiroli A, Simonet P, Frostegard A, Vogel TM, Monier JM (2007) Fate of transgenic plant DNA in the environment. Environ. Biosafety. Res. 6: 15–35
Poulter RT, Goodwin TJ, Butler MI (2007) The nuclear-encoded inteins of fungi. Fungal Genet. Biol. 44: 153–179
Prescott VE, Campbell PM, Moore A, Mattes J, Rothenberg ME, Foster PS, Higgins TJ, Hogan SP (2005) Transgenic expression of bean alpha-amylase inhibitor in peas results in altered structure and immunogenicity. J. Agric. Food Chem. 53: 9023–9030
Ragan MA (2001) Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11: 620–626
Ragan MA, Charlebois, RL (2002) Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission. Int. J. Syst. Evol. Microbiol. 52: 777–787
Ragan MA, Harlo TJ, Beik RG (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol. 14: 4–8
Raja R, Wisle JW, Bell CE (2006) Probing the DNA sequence specificity of Escherichia coli RECA protein. Nucl. Acids Res. 34: 2463–2471
Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306: 1344–1350 CrossRef
Rekab D, Carraro L, Schneider B, Seemller E, Chen J, Chang CJ, Locci R, Firrao G (1999) Geminivirus-related extrachromosomal DNAs of the X-clade phytoplasmas share high sequence similarity. Microbiology 145: 1453–1459 CrossRef
Rest JS, Mindell DP (2003) Retroids in archaea: phylogeny and lateral origins. Mol. Biol. Evol. 20: 1134–1142
Revers F, Le Gall O, Candresse T, Le Romancer M, Dunez J (1996) Frequent occurrence of recombinant potyvirus isolates. J. Gen. Virol. 77: 1953–1965
Rezaian MA (1990) Australian grapevine viroid - evidence for extensive recombination between viroids. Nucleic Acids Res. 18: 1813–1818
Rizzi A, Pontiroli A, Brusetti L, Borin S, Sorlini C, Abruzzese A, Sacchi GA, Vogel TM, Simonet P, Bazzicalupo M, Nielsen KM, Monier JM, Daffonchio D (2008) Strategy for in situ detection of natural transformation-based horizontal gene transfer events. Appl. Environ. Microbiol. 74: 1250–1254
Rogers MB, Patron NJ, Keeling PJ (2007) Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria. BMC Biol. 5: 26–33
Rokyta DR, Burch CL, Caudie SB, Wichman HA (2006) Horizontal gene transfer and the evolution of microvirid coliphage genomes. J. Bacteriol. 188: 1134–1142
Ronchel MC, Ramos-Diaz MA, Ramos JL (2000) Retrotransfer of DNA in the rhizosphere. Environ. Microbiol. 2: 319–323
Rosewich UL, Kistler HC (2000) Role of horizontal gene transfer in the evolution of fungi. Ann. Rev. Phytopath. 38: 325–363
Rossi F, Morlacchini M, Fusconi G, Pietri A, Mazza R, Piva G (2005) Effect of Bt corn on broiler growth performance and fate of feed-derived DNA in the digestive tract. Poult. Sci. 84: 1022–1030
Rowe-Magnus DA, Mazel D (2001) Integrons: natural tools for bacterial genome evolution. Curr. Opin. Microbiol. 4: 565–569
Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, Coster J (2001) Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res. 11: 1404–1409
Sander M, Schmieger H (2001) Method for host-independent detection of generalized transducing bacteriophages in natural habitats. Appl. Environ. Microbiol. 67: 1490–1493
Sandford JC, Johnston SA (1985) The concept of parasite-derived resistance – deriving resistance genes from the parasite's own genome. J. Theor. Biol. 113: 395–405
Schoelz JE, Wintermantel WM (1993) Expansion of viral host range through complementation and recombination in transgenic plants. Plant Cell 5: 1669–1679 CrossRef
Sharma R, Damgaard D, Alexander TW, Dugan ME, Aalhus JL, Stanford K, McAllister TA (2006) Detection of transgenic and endogenous plant DNA in digesta and tissues of sheep and pigs fed Roundup Ready canola meal. J. Agric. Food Chem. 54: 1699–1709
Simpson DJ, Fry JC, Rogers HJ, Day MJ (2007) Transformation of Acinetobacter baylyi in non-sterile soil using recombinant plant nuclear DNA. Environ. Biosafety. Res. 6: 101–112
Smith MW, Feng DF, Doolittle RF (1992) Evolution by acquisition: The case for horizontal gene transfers. Trends Biochem. Sci. 17: 489–493
Snyder LA, McGowan S, Rogers M, Duro E, O'Farrell E, Saunders NJ (2007) The repertoire of minimal mobile elements in the Neisseria species and evidence that these are involved in horizontal gene transfer in other bacteria. Mol. Biol. Evol. 24: 2802–2815
Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 1449–1452
Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nat. Rev. Microbiol. 3: 700–710
Souza V, Travisano M, Turner PE, Eguiarte LE (2002) Does experimental evolution reflect patterns in natural populations? E. coli strains from long-term studies compared with wild isolates. Antonie Leeuwenhoek 81: 143–153
Suzuki K, Yamashita I, Tanaka N (2002) Tobacco plants were transformed by Agrobacterium rhizogenes infection during their evolution. Plant J. 32: 775–787
Syvanen M (1994) Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28: 237–261
Taghavi S, Barac T, Greenberg B, Borremans B, Vangronsveld J, van der Lelie D (2005) Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl. Environ. Microbiol. 71: 8500–8505
Takeshita M, Suzuki M, Takanami Y (2001) Combination of amino acids in the 3a protein and the coat protein of cucumber mosaic virus determines symptom expression and viral spread in bottle gourd. Arch. Virol. 146: 697–711
Tan Z, Wada Y, Chen J, Ohshima K (2004) Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus. J. Gen. Virol. 85: 2683–2696
Taubenberger JK (2006) The origin and virulence of the 1918 “Spanish” influenza virus. Proc. Am. Philos. Soc. 150: 86–112
Thomas CM, Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Rev. Microbiol. 3: 711–721
Thomason B, Read TD (2006) Shuffling bacterial metabolomes. Genome Biol. 7: 204
Tony MA, Butschke A, Broll H, Grohmann L, Zagon J, Halle I, Danicke S, Schauzu M, Hafez HM, Flachowsky G (2003) Safety assessment of Bt 176 maize in broiler nutrition: degradation of maize-DNA and its metabolic fate. Arch. Tierernahr. 57: 235–252
Touchon M, Rocha EPC (2007) Causes of insertion sequences abundance in prokaryotic genomes. Mol. Biol. Evol. 24: 969–981
Tsirigos A, Rigoutsos I (2005) A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res. 33: 922–933
Turturo C, Friscina A, Gaubert S, Jacquemond M, Thompson JR, Tepfer M (2008) Evaluation of potential risks associated with recombination in transgenic plants expressing viral sequences. J. Gen. Virol. 89: 327–335
Tzfira T, Li J, Lacroix B, Citovsky V (2004) Agrobacterium T-DNA integration: molecules and models. Trends Genet. 20: 375–383
Ueno R, Huss VA, Urano N, Watabe S (2007) Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain. Microbiology 153: 3879–3893 CrossRef
USEPA (United States Environmental Protection Agency) (1998) Framework for Ecological Risk Assessment, EPA Office of Research and Development, National Center for Environmental Assessment, Washington Office, Washinton, D.C.
van den Eede G, Aarts H, Buhk HJ, Corthier G, Flint HJ, Hammes W, Jacobsen B, Midtvedt T, van der Vossen, von Wright A, Wackernagel W, Wilcks A (2004) The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants. Food Chem. Toxicol. 42: 1127–1156
van Elsas, JD, Bailey, MJ (2002) The ecology of transfer of mobile genetic elements. FEMS Microbiol. Ecol. 42: 187197 CrossRef
van Elsas, JD, Turner, S, Bailey, MJ (2003) Horizontal gene transfer in the phytosphere. New Phytol. 157: 525537 CrossRef
Vera A, Daros JA, Flores R, Hernandez C (2000) The DNA of a plant retroviroid-like element is fused to different sites in the genome of a plant pararetrovirus and shows multiple forms with sequence deletions. J. Virol. 74: 10390–10400 CrossRef
Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS, Giovannoni SJ (2007) High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ. Microbiol. 9: 2430–2440
Vives MC, Rubio L, Sambade A, Mirkov TE, Moreno P, Guerri J (2005) Evidence of multiple recombination events between two RNA sequence variants within a Citrus tristeza isolate. Virology 331: 232–237 CrossRef
Vlassov V, Laktionov PP, Rykova EY (2007) Extracellular nucleic acids. Bioessays 29: 654–667
Weinbauer MG (2004) Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28: 127–181
Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ. Microbiol. 6: 1–11
Welch RA, Burland V, Plunkett G III, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99: 17020–17024
Weller GR, Kysela B, Roy R, Tonkin LM, Scanlan E, Della M, Devine SK, Day JP, Wilkinson A, d'Adda di Fagagna F, Devine KM, Bowater RP, Jeggo PA, Jackson SP, Doherty AJ (2002) Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297: 1686–1689 CrossRef
Wenzl P, Wong L, Kwang-won K, Jefferson RA (2005) A functional screen identifies lateral transfer of β-glucuronidase (gus) from bacteria to fungi. Mol. Biol. Evol. 22: 308–316
White FF, Garfinkel DJ, Huffman GA, Gordon MP, Nester EW (1983) Sequences homologous to Agrobacterium rhizogenes T-DNA in the genomes of uninfected plants. Nature 301: 348–350
Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118–2120
Wiedemann S, Lutz B, Kurtz H, Schwarz FJ, Albrecht C (2006) In situ studies on the time-dependent degradation of recombinant corn DNA and protein in the bovine rumen. J. Anim Sci. 84: 135–144
Wintermantel WM, Schoelz JE (1996) Isolation of recombinant viruses between cauliflower mosaic virus and a viral gene in transgenic plants under conditions of moderate selection pressure. Virology 223: 156–164
Woese CR (2004) A new biology for a new century. Microbiol. Mol. Biol. Rev. 68: 173–186
Wolska KI (2003) Horizontal DNA transfer between bacteria in the environment. Acta Microbiol. Pol. 52: 233–243
Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol. 80: 2535–2543
Wuertz S, Okabe S, Hausner M (2004) Microbial communities and their interactions in biofilm systems: an overview. Water Sci. Technol. 49: 327–336
Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5: e156
Yamanaka K, Shimamoto T, Inouye S, Inouye M (2002) Retrons. In Craig NL, Craigie R, Gellert M, Lambowitz AM, eds, Mobile DNA II, American Society for Microbiology, pp 784–795
Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181: 5201–5209
Yaron S, Kolling GL, Simon L, Matthews KR (2000) Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl. Environ. Microbiol. 66: 4414–4420
Yin Y, Fischer D (2006) On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. BMC Evol. Biol. 6: 63
Zaneveld JR, Nemergut DR, Knight R (2008) Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology 154: 1–15 CrossRef
Zeidner G, Bielawski JP, Shmoish M, Scanlan DJ, Sabehi G, Béjà O (2005) Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates. Environ. Microbiol. 7: 1505–1513
Zhaxybayeva O, Nesbø CL, Doolittle WF (2007) Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biol. 8: 402–406
Zhou X, Liu Y, Calvert L, Munoz C, Otim-Nape GW, Robinson DJ, Harrison BD (1997) Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J. Gen. Virol. 78: 2101–2111
Zupan J, Muth TR, Draper O, Zambryski P (2000) The transfer of DNA from Agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J. 23: 11–28 CrossRef