Cascales E, Christie PJ (2003) The versatile bacterial type IV secretion
systems. Nat Rev Microbiol 1:137–149
Cavalier-Smith T (1999) Principles of protein and lipid targeting in
secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan
plastid origins and the eukaryote family tree. J Eukaryot Microbiol
46:347–366
Ceremonie H, Buret F, Simonet P, Vogel TM (2004) Isolation of
lightning-competent soil bacteria. Appl Environ Microbiol
70:6342–6346. 509
Chen I, Dubnau D (2004) DNA uptake during bacterial transformation.
Nat Rev Microbiol 2:241–249
Curtis BA et al (2012) Algal genomes reveal evolutionary mosaicism
and the fate of nucleomorphs. Nature 492:59–65
d’Herelle F (1917) The nature of bacteriophage. Br Med 2:289–293
Danner DB, Deich RA, Sisco KL, Smith HO (1980) An eleven-basepair sequence determines the specificity of DNA uptake in
Haemophilus transformation. Gene 11:311–318
Davis BD (1950) Nonfiltrability of the agents of genetic recombination
in Escherichia coli. J Bacteriol 60:507–508
de Vries J, Wackernagel W (2002) Integration of foreign DNA
during natural transformation of Acinetobacter sp. by homologyfacilitated illegitimate recombination. Proc Natl Acad Sci U S A
99:2094–2099
Deppenmeier U et al (2002) The genome of Methanosarcina mazei:
evidence for lateral gene transfer between bacteria and archaea.
J Mol Microbiol Biotechnol 4:453–461
Derelle E et al (2006) Genome analysis of the smallest free-living
eukaryote Ostreococcus tauri unveils many unique features. Proc
Natl Acad Sci U S A 103:11647–11652
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
Doolittle WF, Boucher Y, Nesbo CL, Douady CJ, Andersson JO, Roger
AJ (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; discussion 57–38
Downie AW (1972) Pneumococcal transformation – a backward view.
Fourth Griffith Memorial Lecture. J Gen Microbiol 73:1–11
Duckworth DH (1976) Who discovered bacteriophage? Bacteriol Rev
40:793–802
Eichinger L et al (2005) The genome of the social amoeba
Dictyostelium discoideum. Nature 435:43–57
Esser C et al (2004) A genome phylogeny for mitochondria among
alpha-proteobacteria and a predominantly eubacterial ancestry of
yeast nuclear genes. Mol Biol Evol 21:1643–1660
Forterre P (2002) A hot story from comparative genomics: reverse
gyrase is the only hyperthermophile-specific protein. Trends
Genet 18:236–237
Forterre P, Bouthier De La Tour C, Philippe H, Duguet M (2000)
Reverse gyrase from hyperthermophiles: probable transfer of a
thermoadaptation trait from Archaea to Bacteria. Trends Genet
16:152–154
Friesen TL et al (2006) Emergence of a new disease as a result of
interspecific virulence gene transfer. Nat Genet 38:953–956
Futterer O et al (2004) Genome sequence of Picrophilus torridus and its
implications for life around pH 0. Proc Natl Acad Sci U S A
101:9091–9096
Garcia-Vallve S, Romeu A, Palau J (2000) Horizontal gene transfer
of glycosyl hydrolases of the rumen fungi. Mol Biol Evol
17:352–361
Gautier C (2000) Compositional bias in DNA. Curr Opin Genet Dev
10:656–661
Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genomescale estimates of horizontal gene transfer. PLoS Biol 3:e316
Gilmour MW, Thomson NR, Sanders M, Parkhill J, Taylor DE (2004)
The complete nucleotide sequence of the resistance plasmid R478:
defining the backbone components of incompatibility group H
conjugative plasmids through comparative genomics. Plasmid
52:182–202
Goodman SD, Scocca JJ (1988) Identification and arrangement of the
DNA sequence recognized in specific transformation of Neisseria
gonorrhoeae. Proc Natl Acad Sci U S A 85:6982–6986
Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with
gene expressivity. Nucleic Acids Res 10:7055–7074
Griffith MB (1928) The significance of pneumococcal types. J Hygiene
27:113–159
Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene
transfer to the evolution of Saccharomyces cerevisiae. Eukaryot
Cell 4:1102–1115
Hallam SJ et al (2006) Genomic analysis of the uncultivated marine
crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A
103:18296–18301
Hayashi T et al (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison
with a laboratory strain K-12. DNA Res 8:11–22
Heinemann JA, Sprague GF Jr (1989) Bacterial conjugative plasmids
mobilize DNA transfer between bacteria and yeast. Nature
340:205–209
Hotopp JC et al (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753–1756
Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS,
Kissinger JC (2004) Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol 5:R88
Ikeda H, Shiraishi K, Ogata Y (2004) Illegitimate recombination
mediated by double-strand break and end-joining in Escherichia
coli. Adv Biophys 38:3–20
Inderbitzin P, Harkness J, Turgeon BG, Berbee ML (2005) Lateral transfer of mating system in Stemphylium. Proc Natl Acad Sci U S A
102:11390–11395
Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic
evolution. Nat Rev Genet 9:605–618
Kennedy SP, Ng WV, Salzberg SL, Hood L, Das- Sarma S (2001)
Understanding the adaptation of Halobacterium species NRC-1 to
its extreme environment through computational analysis of its
genome sequence. Genome Res 11:1641–1650
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
Lambert PA (2005) Bacterial resistance to antibiotics: modified target
sites. Adv Drug Deliv Rev 57:1471–1485
Lan R, Reeves PR (1996) Gene transfer is a major factor in bacterial
evolution. Mol Biol Evol 13:47–55
Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the
need for a species genome concept. Trends Microbiol 8:396–401
Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes:
rates of change and exchange. J Mol Evol 44:383–397
Lawrence JG, Ochman H (1998) Molecular archaeology of the
Escherichia coli genome. Proc Natl Acad Sci U S A 95:9413–9417
Lederberg J (1947) Gene recombination and linked segregations in
Escherichia Coli. Genetics 32:505–525
Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal
phylogeny in prokaryotes: the case of the gamma-Proteobacteria.
PLoS Biol 1:E19
Livermore D (2004) Can better prescribing turn the tide of resistance?
Nat Rev Microbiol 2:73–78
Livermore DM, Woodford N (2000) Carbapenemases: a problem in
waiting? Curr Opin Microbiol 3:489–495
Lopez-Garcia P, Brochier C, Moreira D, Rodriguez- Valera F (2004)
Comparative analysis of a genome fragment of an uncultivated
480
C. Brochier-Armanet and D. Moreira
systems. Nat Rev Microbiol 1:137–149
Cavalier-Smith T (1999) Principles of protein and lipid targeting in
secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan
plastid origins and the eukaryote family tree. J Eukaryot Microbiol
46:347–366
Ceremonie H, Buret F, Simonet P, Vogel TM (2004) Isolation of
lightning-competent soil bacteria. Appl Environ Microbiol
70:6342–6346. 509
Chen I, Dubnau D (2004) DNA uptake during bacterial transformation.
Nat Rev Microbiol 2:241–249
Curtis BA et al (2012) Algal genomes reveal evolutionary mosaicism
and the fate of nucleomorphs. Nature 492:59–65
d’Herelle F (1917) The nature of bacteriophage. Br Med 2:289–293
Danner DB, Deich RA, Sisco KL, Smith HO (1980) An eleven-basepair sequence determines the specificity of DNA uptake in
Haemophilus transformation. Gene 11:311–318
Davis BD (1950) Nonfiltrability of the agents of genetic recombination
in Escherichia coli. J Bacteriol 60:507–508
de Vries J, Wackernagel W (2002) Integration of foreign DNA
during natural transformation of Acinetobacter sp. by homologyfacilitated illegitimate recombination. Proc Natl Acad Sci U S A
99:2094–2099
Deppenmeier U et al (2002) The genome of Methanosarcina mazei:
evidence for lateral gene transfer between bacteria and archaea.
J Mol Microbiol Biotechnol 4:453–461
Derelle E et al (2006) Genome analysis of the smallest free-living
eukaryote Ostreococcus tauri unveils many unique features. Proc
Natl Acad Sci U S A 103:11647–11652
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
Doolittle WF, Boucher Y, Nesbo CL, Douady CJ, Andersson JO, Roger
AJ (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; discussion 57–38
Downie AW (1972) Pneumococcal transformation – a backward view.
Fourth Griffith Memorial Lecture. J Gen Microbiol 73:1–11
Duckworth DH (1976) Who discovered bacteriophage? Bacteriol Rev
40:793–802
Eichinger L et al (2005) The genome of the social amoeba
Dictyostelium discoideum. Nature 435:43–57
Esser C et al (2004) A genome phylogeny for mitochondria among
alpha-proteobacteria and a predominantly eubacterial ancestry of
yeast nuclear genes. Mol Biol Evol 21:1643–1660
Forterre P (2002) A hot story from comparative genomics: reverse
gyrase is the only hyperthermophile-specific protein. Trends
Genet 18:236–237
Forterre P, Bouthier De La Tour C, Philippe H, Duguet M (2000)
Reverse gyrase from hyperthermophiles: probable transfer of a
thermoadaptation trait from Archaea to Bacteria. Trends Genet
16:152–154
Friesen TL et al (2006) Emergence of a new disease as a result of
interspecific virulence gene transfer. Nat Genet 38:953–956
Futterer O et al (2004) Genome sequence of Picrophilus torridus and its
implications for life around pH 0. Proc Natl Acad Sci U S A
101:9091–9096
Garcia-Vallve S, Romeu A, Palau J (2000) Horizontal gene transfer
of glycosyl hydrolases of the rumen fungi. Mol Biol Evol
17:352–361
Gautier C (2000) Compositional bias in DNA. Curr Opin Genet Dev
10:656–661
Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genomescale estimates of horizontal gene transfer. PLoS Biol 3:e316
Gilmour MW, Thomson NR, Sanders M, Parkhill J, Taylor DE (2004)
The complete nucleotide sequence of the resistance plasmid R478:
defining the backbone components of incompatibility group H
conjugative plasmids through comparative genomics. Plasmid
52:182–202
Goodman SD, Scocca JJ (1988) Identification and arrangement of the
DNA sequence recognized in specific transformation of Neisseria
gonorrhoeae. Proc Natl Acad Sci U S A 85:6982–6986
Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with
gene expressivity. Nucleic Acids Res 10:7055–7074
Griffith MB (1928) The significance of pneumococcal types. J Hygiene
27:113–159
Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene
transfer to the evolution of Saccharomyces cerevisiae. Eukaryot
Cell 4:1102–1115
Hallam SJ et al (2006) Genomic analysis of the uncultivated marine
crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A
103:18296–18301
Hayashi T et al (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison
with a laboratory strain K-12. DNA Res 8:11–22
Heinemann JA, Sprague GF Jr (1989) Bacterial conjugative plasmids
mobilize DNA transfer between bacteria and yeast. Nature
340:205–209
Hotopp JC et al (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753–1756
Huang J, Mullapudi N, Lancto CA, Scott M, Abrahamsen MS,
Kissinger JC (2004) Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol 5:R88
Ikeda H, Shiraishi K, Ogata Y (2004) Illegitimate recombination
mediated by double-strand break and end-joining in Escherichia
coli. Adv Biophys 38:3–20
Inderbitzin P, Harkness J, Turgeon BG, Berbee ML (2005) Lateral transfer of mating system in Stemphylium. Proc Natl Acad Sci U S A
102:11390–11395
Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic
evolution. Nat Rev Genet 9:605–618
Kennedy SP, Ng WV, Salzberg SL, Hood L, Das- Sarma S (2001)
Understanding the adaptation of Halobacterium species NRC-1 to
its extreme environment through computational analysis of its
genome sequence. Genome Res 11:1641–1650
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
Lambert PA (2005) Bacterial resistance to antibiotics: modified target
sites. Adv Drug Deliv Rev 57:1471–1485
Lan R, Reeves PR (1996) Gene transfer is a major factor in bacterial
evolution. Mol Biol Evol 13:47–55
Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the
need for a species genome concept. Trends Microbiol 8:396–401
Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes:
rates of change and exchange. J Mol Evol 44:383–397
Lawrence JG, Ochman H (1998) Molecular archaeology of the
Escherichia coli genome. Proc Natl Acad Sci U S A 95:9413–9417
Lederberg J (1947) Gene recombination and linked segregations in
Escherichia Coli. Genetics 32:505–525
Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal
phylogeny in prokaryotes: the case of the gamma-Proteobacteria.
PLoS Biol 1:E19
Livermore D (2004) Can better prescribing turn the tide of resistance?
Nat Rev Microbiol 2:73–78
Livermore DM, Woodford N (2000) Carbapenemases: a problem in
waiting? Curr Opin Microbiol 3:489–495
Lopez-Garcia P, Brochier C, Moreira D, Rodriguez- Valera F (2004)
Comparative analysis of a genome fragment of an uncultivated
480
C. Brochier-Armanet and D. Moreira