Genome Research Econo tag

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Garcia-Vallvé, S.
Right arrow Articles by Palau, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Garcia-Vallvé, S.
Right arrow Articles by Palau, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 10, Issue 11, 1719-1725, November 2000

LETTER
Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes

Santiago Garcia-Vallvé, Anton Romeu,1 and Jaume Palau

Rovira i Virgili University, Department of Biochemistry and Biotechnology, E-43005 Tarragona, Catalonia, Spain

There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.

1 Corresponding author.

10:1719-1725 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
M. J. Lercher and C. Pal
Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years
Mol. Biol. Evol., March 1, 2008; 25(3): 559 - 567.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Puigbo, A. Romeu, and S. Garcia-Vallve
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D524 - D527.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
B. G. Butcher, Y.-P. Lin, and J. D. Helmann
The yydFGHIJ Operon of Bacillus subtilis Encodes a Peptide That Induces the LiaRS Two-Component System
J. Bacteriol., December 1, 2007; 189(23): 8616 - 8625.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Becq, M. C. Gutierrez, V. Rosas-Magallanes, J. Rauzier, B. Gicquel, O. Neyrolles, and P. Deschavanne
Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli
Mol. Biol. Evol., August 1, 2007; 24(8): 1861 - 1871.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. Linz, A. Radtke, and A. von Haeseler
A Likelihood Framework to Measure Horizontal Gene Transfer
Mol. Biol. Evol., June 1, 2007; 24(6): 1312 - 1319.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Feng and E. R.M. Tillier
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
Bioinformatics, May 15, 2007; 23(10): 1195 - 1202.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J.-M. Hu, H.-C. Fu, C.-H. Lin, H.-J. Su, and H.-H. Yeh
Reassortment and Concerted Evolution in Banana Bunchy Top Virus Genomes
J. Virol., February 15, 2007; 81(4): 1746 - 1761.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
S. P. Duffy, A. M. Young, B. Morin, C. J. Lucarotti, B. F. Koop, and D. B. Levin
Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome
J. Virol., July 15, 2006; 80(14): 6952 - 6963.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
W. Hao and G. B. Golding
The fate of laterally transferred genes: Life in the fast lane to adaptation or death.
Genome Res., May 1, 2006; 16(5): 636 - 643.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. T. R. Vasconcelos, H. B. Ferreira, C. V. Bizarro, S. L. Bonatto, M. O. Carvalho, P. M. Pinto, D. F. Almeida, L. G. P. Almeida, R. Almeida, L. Alves-Filho, et al.
Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae
J. Bacteriol., August 15, 2005; 187(16): 5568 - 5577.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
L. Charles, I. Carbone, K. G. Davies, D. Bird, M. Burke, B. R. Kerry, and C. H. Opperman
Phylogenetic Analysis of Pasteuria penetrans by Use of Multiple Genetic Loci
J. Bacteriol., August 15, 2005; 187(16): 5700 - 5708.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Tsirigos and I. Rigoutsos
A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes
Nucleic Acids Res., July 8, 2005; 33(12): 3699 - 3707.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Fertil, M. Massin, S. Lespinats, C. Devic, P. Dumee, and A. Giron
GENSTYLE: exploration and analysis of DNA sequences with genomic signature
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W512 - W515.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J.-F. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann, and G. Perriere
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Bioinformatics, June 1, 2005; 21(11): 2596 - 2603.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
E. Belda, A. Moya, and F. J. Silva
Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria
Mol. Biol. Evol., June 1, 2005; 22(6): 1456 - 1467.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Ochman, E. Lerat, and V. Daubin
Examining bacterial species under the specter of gene transfer and exchange
PNAS, May 3, 2005; 102(suppl_1): 6595 - 6599.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. A. Suchard
Stochastic Models for Horizontal Gene Transfer: Taking a Random Walk Through Tree Space
Genetics, May 1, 2005; 170(1): 419 - 431.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Dufraigne, B. Fertil, S. Lespinats, A. Giron, and P. Deschavanne
Detection and characterization of horizontal transfers in prokaryotes using genomic signature
Nucleic Acids Res., January 13, 2005; 33(1): e6 - e6.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Medrano-Soto, G. Moreno-Hagelsieb, P. Vinuesa, J. A. Christen, and J. Collado-Vides
Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes
Mol. Biol. Evol., October 1, 2004; 21(10): 1884 - 1894.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
H. Christensen, P. Kuhnert, J. E. Olsen, and M. Bisgaard
Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae
Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1601 - 1609.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
W. Hao and G. B. Golding
Patterns of Bacterial Gene Movement
Mol. Biol. Evol., July 1, 2004; 21(7): 1294 - 1307.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. dos Reis, L. Wernisch, and R. Savva
Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
Nucleic Acids Res., December 1, 2003; 31(23): 6976 - 6985.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H. Westers, R. Dorenbos, J. M. van Dijl, J. Kabel, T. Flanagan, K. M. Devine, F. Jude, S. J. Seror, A. C. Beekman, E. Darmon, et al.
Genome Engineering Reveals Large Dispensable Regions in Bacillus subtilis
Mol. Biol. Evol., December 1, 2003; 20(12): 2076 - 2090.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
V. Kunin and C. A. Ouzounis
The Balance of Driving Forces During Genome Evolution in Prokaryotes
Genome Res., July 1, 2003; 13(7): 1589 - 1594.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
P. van Berkum, Z. Terefework, L. Paulin, S. Suomalainen, K. Lindstrom, and B. D. Eardly
Discordant Phylogenies within the rrn Loci of Rhizobia
J. Bacteriol., May 15, 2003; 185(10): 2988 - 2998.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
V. Daubin and G. Perriere
G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes
Mol. Biol. Evol., April 1, 2003; 20(4): 471 - 483.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
Nucleic Acids Res., January 1, 2003; 31(1): 187 - 189.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
P. Lio
Investigating the Relationship Between Genome Structure, Composition, and Ecology in Prokaryotes
Mol. Biol. Evol., June 1, 2002; 19(6): 789 - 800.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
G. D. P. Clarke, R. G. Beiko, M. A. Ragan, and R. L. Charlebois
Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores
J. Bacteriol., April 15, 2002; 184(8): 2072 - 2080.
[Abstract] [Full Text]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Akashi and T. Gojobori
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
PNAS, March 19, 2002; 99(6): 3695 - 3700.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
I. Serganova, V. Ksenzenko, A. Serganov, I. Meshcheryakova, M. Pyatibratov, O. Vakhrusheva, A. Metlina, and O. Fedorov
Sequencing of Flagellin Genes from Natrialba magadii Provides New Insight into Evolutionary Aspects of Archaeal Flagellins
J. Bacteriol., January 1, 2002; 184(1): 318 - 322.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. G. DelVecchio, V. Kapatral, R. J. Redkar, G. Patra, C. Mujer, T. Los, N. Ivanova, I. Anderson, A. Bhattacharyya, A. Lykidis, et al.
The genome sequence of the facultative intracellular pathogen Brucella melitensis
PNAS, December 21, 2001; (2001) 221575398.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. A. Israel, N. Salama, U. Krishna, U. M. Rieger, J. C. Atherton, S. Falkow, and R. M. Peek Jr.
Helicobacter pylori genetic diversity within the gastric niche of a single human host
PNAS, November 20, 2001; (2001) 251551698.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. J. Janssen, B. Audit, and C. A. Ouzounis
Strain-specific genes of Helicobacter pylori: distribution, function and dynamics
Nucleic Acids Res., November 1, 2001; 29(21): 4395 - 4404.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. Klein, M. Friedrich, A. J. Roger, P. Hugenholtz, S. Fishbain, H. Abicht, L. L. Blackall, D. A. Stahl, and M. Wagner
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes
J. Bacteriol., October 15, 2001; 183(20): 6028 - 6035.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. Sandberg, G. Winberg, C.-I. Branden, A. Kaske, I. Ernberg, and J. Coster
Capturing Whole-Genome Characteristics in Short Sequences Using a Naive Bayesian Classifier
Genome Res., August 1, 2001; 11(8): 1404 - 1409.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. G. DelVecchio, V. Kapatral, R. J. Redkar, G. Patra, C. Mujer, T. Los, N. Ivanova, I. Anderson, A. Bhattacharyya, A. Lykidis, et al.
The genome sequence of the facultative intracellular pathogen Brucella melitensis
PNAS, January 8, 2002; 99(1): 443 - 448.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. A. Israel, N. Salama, U. Krishna, U. M. Rieger, J. C. Atherton, S. Falkow, and R. M. Peek Jr.
Helicobacter pylori genetic diversity within the gastric niche of a single human host
PNAS, December 4, 2001; 98(25): 14625 - 14630.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.