Mosaic graphs and comparative genomics in phage communities

Journal of Computational Biology

Volumn 17, Issue 9, 2010, Pages 1315-1326

  Belcaid, Mahdi ^a   Bergeron, Anne ^b   Poisson, Guylaine ^a  

^a University of Hawaii at Manoa   (United States)

^b UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

algorithms; combinatorics; functional genomics

Indexed keywords

ARTICLE; BACTERIOPHAGE; BACTERIUM; GENETIC RECOMBINATION; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; VIROLOGY; VIRUS GENOME;

BACTERIA; BACTERIOPHAGES; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENOME, VIRAL; GENOMICS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT;

STAPHYLOCOCCUS AUREUS;

EID: 77958065837     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0108     Document Type: Article

References (20)

1. Altschul, S. F., Gish, W., Miller, W., et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Bentley, D. R. 2006. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545-552.
3. Breitbart, M., Miyake, J. H., and Rohwer, F. 2004. Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol. Lett. 236, 249-256.
4. Bryan, M. J., Burroughs, N. J., Spence, E. M., et al. 2008. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. PLoS ONE 3, e2048.
5. Glazko, G., Makarenkov, V., Liu, J., et al. 2007. Evolutionary history of bacteriophages with double-stranded DNA genomes. Biol. Direct 2, 36.
6. Gusfield, D., and Bansal, V. 2005. A fundamental decomposition theory for phylogenetic networks and incompatible characters. Lect. Notes Comput. Sci. 3500, 217-232.
7. Hatfull, G. F. 2008. Bacteriophage genomics. Curr. Opin. Microbiol. 11, 447-453.
8. Hatfull, G. F., Cresawn, S. G., and Hendrix, R. W. 2008. Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res. Microbiol. 159, 332-339.
9. Hatfull, G. F., Pedulla, M. L., Jacobs-Sera, D., et al. 2006. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2, e92.
10. Hendrix, R. W. 2002. Bacteriophages: evolution of the majority. Theor. Popul. Biol. 61, 471-480.
11. Highton, P. J., Chang, Y., and Myers, R. J. 1990. Evidence for the exchange of segments between genomes during the evolution of lambdoid bacteriophages. Mol. Microbiol. 4, 1329-1340.
12. Huson, D. H., and Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267.
13. Kurtz, S., Choudhuri, J., Ohlebusch, E., et al. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29, 4633-4642.
14. Kwan, T., Liu, J., DuBow, M., et al. 2005. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc. Natl. Acad. Sci. U. S. A. 102, 5174-5179.
15. Lima-Mendez, G., Van Helden, J., Toussaint, A., et al. 2008. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 25, 762-777.
16. Margulies, M., Egholm, M., Altman, W. E., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.
17. Martinsohn, J. T., Radman, M., and Petit, M. A. 2008. The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet. 4, e1000065.
18. Nesbo, C. L., Dlutek, M., and Ford Dolittle, W. 2006. Recombination in thermotoga: implications for species concepts and biogeography. Genetics 172, 759-769.
19. Rohwer, F., and Edwards, R. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol. 184, 4529-4535.
20. Short, C. M., and Suttle, C. A., 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl. Environ. Microbiol. 71, 480-486.