Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 31, 2009, Pages 12826-12831

  Wu, Guohong Albert ^a,b   Jun, Se Ran ^a   Sims, Gregory E ^a,b   Kim, Sung Hou ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Alignment free genome comparison; Feature frequency profile; Horizontal gene transfer; Virus phylogeny; Whole genome phylogeny

Indexed keywords

DOUBLE STRANDED DNA; PROTEOME; VIRUS DNA;

ARTICLE; CLADISTICS; DNA VIRUS; EUKARYOTE; EVOLUTION; HERPES VIRUS; HORIZONTAL GENE TRANSFER; INTERMETHOD COMPARISON; NONHUMAN; PHYCODNAVIRIDAE; PHYLOGENY; POPULATION; PRIORITY JOURNAL; TAXONOMIC RANK; VIRUS GENE; BACULOVIRUS; CLASSIFICATION; GENETICS; POXVIRUS; SEQUENCE ALIGNMENT;

EUKARYOTA; HERPESVIRIDAE; MIMIVIRUS; PHYCODNAVIRIDAE; UNCLASSIFIED VIRUSES;

BACULOVIRIDAE; DNA VIRUSES; GENE TRANSFER, HORIZONTAL; HERPESVIRIDAE; PHYCODNAVIRIDAE; PHYLOGENY; POXVIRIDAE; PROTEOME; SEQUENCE ALIGNMENT;

EID: 69149103357     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0905115106     Document Type: Article

References (48)

1. Herniou EA, Jehle JA (2007) Baculovirus phylogeny and evolution. Curr Drug Targets 8:1043-1050.
2. Montague MG, Hutchison CA, 3rd (2000) Gene content phylogeny of herpesviruses. Proc Natl Acad Sci USA 97:5334-5339.
3. McLysaght A, Baldi PF, Gaut BS (2003) Extensive gene gain associated with adaptive evolution of poxviruses. Proc Natl Acad Sci USA 100:15655-15660.
4. de Andrade Zanotto PM, Krakauer DC (2008) Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites. PLoSONE 3:e3500.
5. Iyer LM, Aravind L, Koonin EV (2001) Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 75:11720-11734.
6. Marra MA, et al. (2003) The Genome sequence of the SARS-associated coronavirus. Science 300:1399-1404.
7. Shackelton LA, Holmes EC (2004) The evolution of large DNA viruses: Combining genomic information of viruses and their hosts. Trends Microbiol 12:458-465.
8. Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: Patterns and determinants. Nat Rev Genet 9:267-276.
9. Fauquet CM (2005) Virus Taxonomy: Classification and Nomenclature of Viruses: Eighth Report of the International Committee on the Taxonomy of Viruses (Elsevier, San Diego).
10. Wong KM, Suchard MA, Huelsenbeck JP (2008) Alignment uncertainty and genomic analysis. Science 319:473-476.
11. Vinga S, Almeida J (2003) Alignment-free sequence comparison - a review. Bioinformatics 19:513-523.
12. Hohl M, Ragan MA (2007) Is multiple-sequence alignment required for accurate inference of phylogeny? Syst Biol 56:206-221.
13. Stuart G, Moffett K, Bozarth RF (2004) A whole genome perspective on the phylogeny of the plant virus family Tombusviridae. Arch Virol 149:1595-1610.
14. Yang AC, Goldberger AL, Peng CK (2005) Genomic classification using an information-based similarity index: Application to the SARS coronavirus. J Comp Biol 12:1103-1116.
15. Gao L, Qi J (2007) Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol Biol 7:41.
16. Ulitsky I, Burstein D, Tuller T, Chor B (2006) The average common substring approach to phylogenomic reconstruction. J Comp Biol 13:336-350.
17. Pride DT, Wassenaar TM, Ghose C, Blaser MJ (2006) Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genomics 7:8.
18. Gatherer D (2007) Genome signatures, self-organizing maps and higher order phylogenies: A parametric analysis. Evol Bioinf 3:211-236.
19. Monier A, Claverie JM, Ogata H (2007) Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses. BMC Genomics 8:456.
20. Filee J, Pouget N, Chandler M (2008) Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. BMC Evol Biol 8:320.
21. Hughes AL, Friedman R (2005) Poxvirus genome evolution by gene gain and loss. Mol Phylogenet Evol 35:186-195.
22. Bratke KA, McLysaght (2008) A Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evol Biol 8:67.
23. Sims GE, Jun SR, Wu GA, Kim SH (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci USA 106:2677-2682.
24. Pruitt KD, Tatusova T, Maglott DR (2007) NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35:D61-65.
25. Lin J (1991) Divergence measures based on the Shannon entropy. IEEE T Inform Theory 37:145-151.
26. Bideshi DK, et al. (2003) Phylogenetic analysis and possible function of bro-like genes, a multigene family widespread among large double-stranded DNA viruses of invertebrates and bacteria. J Gen Virol 84:2531-2544.
27. Stasiak K, et al. (2003) Evidence for the evolution of ascoviruses from iridoviruses. J Gen Virol 84:2999-3009.
28. Jehle JA, et al. (2006) On the classification and nomenclature of baculoviruses: A proposal for revision. Arch Virol 151:1257-1266.
29. Jehle JA (2004) The mosaic structure of the polyhedrin gene of the Autographa californica nucleopolyhedrovirus (AcMNPV). Virus Genes 29:5-8.
30. Davison AJ, et al. (2009) The order Herpesvirales. Arch Virol 154:171-177.
31. McGeoch DJ, Rixon FJ, Davison AJ (2006) Topics in herpesvirus genomics and evolution. Virus Res 117:90-104.
32. McGeoch DJ, Gatherer D, Dolan A (2005) On phylogenetic relationships among major lineages of the Gammaherpesvirinae. J Gen Virol 86:307-316.
33. Derelle E, et al. (2008) Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri. PLoS ONE 3:e2250.
34. Larsen JB, Larsen A, Bratbak G, Sandaa RA (2008) Phylogenetic analysis of members of the Phycodnaviridae virus family, using amplified fragments of the major capsid protein gene. Appl Environ Microbiol 74:3048-3057.
35. Monier A, et al. (2008) Marine mimivirus relatives are probably large algal viruses. Virol J 5:12.
36. Raoult D, et al. (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306:1344-1350.
37. Dunigan DD, Fitzgerald LA, Van Etten JL (2006) Phycodnaviruses: A peek at genetic diversity. Virus Res 117:119-132.
38. Allen MJ, Schroeder DC, Holden MT, Wilson WH (2006) Evolutionary history of the Coccolithoviridae. Mol Biol Evol 23:86-92.
39. Lefkowitz EJ, Wang C, Upton C (2006) Poxviruses: Past, present and future. Virus Res 117:105-118.
40. Wang Y, Kleespies RG, Huger AM, Jehle JA (2007) The genome of Gryllus bimaculatus nudivirus indicates an ancient diversification of baculovirus-related nonoccluded nudiviruses of insects. J Virol 81:5395-5406.
41. Garcia-Maruniak A, et al. (2009) Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade. J Gen Virol 90:334-346.
42. Kullback S, Leibler RA (1951) On information and sufficiency. Ann Math Stat 22:79-86.
43. Sadovsky MG (2003) Comparison of real frequencies of strings vs. the expected ones reveals the information capacity of macromoleculae. J Biol Phys 29:23-38.
44. Wootton JC, Federhen S (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comp Chem 17:149-163.
45. Gascuel O (1997) BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685-695.
46. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
47. Alfaro ME, Zoller S, Lutzoni F (2003) Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20:255-266.
48. Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128.