Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach

Journal of Molecular Evolution

Volumn 58, Issue 1, 2004, Pages 1-11

  Qi, Ji ^a,b   Wang, Bin ^a   Hao, Bai Iin ^a  

^a INSTITUTE OF THEORETICAL PHYSICS   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

Archaea; Compositional distance; K strings; Phylogeny; Prokaryote; Tree of life

Indexed keywords

OLIGOPEPTIDE; PROTEOME;

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARABIDOPSIS; ARCHAEBACTERIUM; ARTICLE; BACILLUS; BACTERIAL STRAIN; CAENORHABDITIS ELEGANS; ENCEPHALITOZOON CUNICULI; GENE FREQUENCY; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DISTANCE; LACTOBACILLUS; LACTOCOCCUS LACTIS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PLASMODIUM FALCIPARUM; PROKARYOTE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STREPTOCOCCACEAE; UNINDEXED SEQUENCE; YEAST;

ALGORITHMS; ARCHAEA; BACTERIA; CLASSIFICATION; DATABASES, NUCLEIC ACID; OLIGOPEPTIDES; PHYLOGENY;

ARABIDOPSIS; ARCHAEA; BACTERIA (MICROORGANISMS); CAENORHABDITIS; CAENORHABDITIS ELEGANS; ENCEPHALITOZOON CUNICULI; EUKARYOTA; LACTOBACILLUS; LACTOCOCCUS LACTIS; PLASMODIUM FALCIPARUM; PROKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE; STREPTOCOCCACEAE; STREPTOCOCCUS;

EID: 1242335920     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2493-7     Document Type: Article

References (34)

1. Alberts B, et al. (1994) Molecular biology of the cell, 3rd ed. Garland, New York, p 121 and references therein
2. 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
3. Baldauf SL, Palmer JD, Doolittle WF (1996) The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc Natl Acad Sci USA 93:7749-7754
4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2003) GenBank. Nucleic Acid Res 31:23-27 (Available at ftp://ncbi.nlm.nih.gov/genbank/ genomes/Bacteria/)
5. Bergey's Manual Trust (1984-1989) Bergey's manual of systematic bacteriology, 1st ed, Vois 1-4. Williams & Wilkins, Baltimore
6. Bergey's Manual Trust (2001) Bergey's manual of systematic bacteriology, 2nd ed, Vol 1. Springer-Verlag, New York
7. Brendel V, Beckmann JS, Trifonov EN (1986) Linguistics of nucleotide sequences: Morphology and comparison of vocabularies. J Biomol Struct Dyn 4:11-21
8. Chu K, Qi J, Yu Z, Anh VO (2003) Origin and phylogeny of chloroplasts: A simple correlation analysis of complete genomes. Mol Biol Evol (in press)
9. Daubin V, Gouy M, Perriere G (2001) Bacterial molecular phylogeny using supertree approach. Genome Inform 12:155-164
10. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2128
11. Doolittle WF (2000) Uprooting the tree of life. Sci Am February pp 90-95
12. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author at http://evolution. genetics.washington.edu/phylip. html
13. Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganism. Nucleic Acid Res 27:4218-4222
14. Garrity GM, Winters M, Searles DB (2001) Taxonomic outline of the prokaryotic genera. In: Bergey's manual of systematic bacteriology, 2nd ed, Rel 1.0 (Available at http://www.cme. msu.edu/bergeys/april2001-genus.pdf)
15. Hao BL, Xie HM, Zhang SY (2001) Compositional representation of protein sequences and the number of Eulerian loops. (Available at arXiv:physics/0103028 at: http://lanl.arXiv.org/)
16. Hu R, Wang B (2001) Statistically significant strings are related to regulatory elements in the promoter region of Saccharomyces cerevisiae. Physica A 290:464-474
17. Huynen MA, Snel B, Bork P (1999) Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science 286:1441
18. Karlin S, Burge C (1995) Dinucleotide relative abundance extremes: A genomic signature. Trends Genet 11:283-290
19. Margulis LM, Schwartz KV (1998) Five kingdoms, 3rd ed. WH Freeman, New York, p 60
20. Matte-Tailliez O, Brochier C, Forterre P, Philippe H (2002) Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 19:631-639
21. Murray RGE (1989) The higher taxa, or, a place for everything...? In: Williams ST, Sharpe ME, Holt JG (eds) Bergey's manual of systematic bacteriology, Vol 4. Williams and Wilkins, Baltimore, pp 2329-2332
22. Pennisi E (1998) Genome data shake tree of life. Science 280:672-674
23. Pennisi E (1999) Is it time to uproot the tree of life? Science 284:1305-1308
24. Ragan MA (2001) Detection of lateral gene transfer among microbial genomes. Curr Opin Gen Dev 11:620-626
25. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
26. Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nature Genet 21:108-110
27. Tekaia F, Lazcano A, Dujon B (1999) The genomic tree as revealed from whole genome proteome comparisons. Genome Res 9:550-557
28. Tomb JF, White O, Kerlavage AR, et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pyroli. Nature 388:539-547
29. Wheeler DL, Church DM, Federhen S, et al. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31 28-33 (The NCBI-curated prokaryote genomes are available at ftp://ftp.ncbi.nih.gov/genomes/ Bacteria/. The NCBI Taxonomy Browser is located at http://www.ncbi.nlm. nih.gov/Taxonomy/taxonomyhome.html
30. Woese CR (1998) The universal ancester. Proc Natl Acad Sci USA 95:6854-6859
31. Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97:8392-8396
32. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090
33. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8 (Available at http://www.biomedcentral.com/1471-2148/ 18)
34. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97-166