메뉴 건너뛰기




Volumn 55, Issue 22, 2010, Pages 2323-2328

Whole-genome based Archaea phylogeny and taxonomy: A composition vector approach

Author keywords

16S rRNA analysis; alignment free; Archaea; composition vector; CVTree; phylogeny; taxonomy

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; FUNGI;

EID: 77955521875     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-010-3008-8     Document Type: Article
Times cited : (5)

References (22)
  • 1
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: the primary kingdoms
    • Woese C R, Fox G E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA, 1977, 74: 5088-5090.
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 2
    • 77955542236 scopus 로고    scopus 로고
    • Bergey's Manual Trust. Bergey's Manual of Systematic Bacteriology. 2nd ed. New York: Springer-Verlag, 2001.
  • 4
    • 24944587193 scopus 로고    scopus 로고
    • Towards a genome-based taxonomy for prokaryotes
    • Konstantinidis K T, Tiedje K V. Towards a genome-based taxonomy for prokaryotes. J Bacteriol, 2005, 187: 6258-6264.
    • (2005) J Bacteriol , vol.187 , pp. 6258-6264
    • Konstantinidis, K.T.1    Tiedje, K.V.2
  • 5
    • 1242335920 scopus 로고    scopus 로고
    • Whole-proteome prokaryote phylogeny without sequence alignment: A K-string composition approach
    • Qi J, Wang B, Hao B L. Whole-proteome prokaryote phylogeny without sequence alignment: A K-string composition approach. J Mol Evol, 2004, 58: 1-11.
    • (2004) J Mol Evol , vol.58 , pp. 1-11
    • Qi, J.1    Wang, B.2    Hao, B.L.3
  • 6
    • 3242889314 scopus 로고    scopus 로고
    • Prokaryote phylogeny without sequence alignment: From avoidance signature to composition distance
    • Hao B L, Qi J. Prokaryote phylogeny without sequence alignment: From avoidance signature to composition distance. J Bioinf Comput Biol, 2004, 2: 1-19.
    • (2004) J Bioinf Comput Biol , vol.2 , pp. 1-19
    • Hao, B.L.1    Qi, J.2
  • 7
    • 1242268097 scopus 로고    scopus 로고
    • Molecular phylogeny of coronaviruses including human SARS-CoV
    • Gao L, Qi J, Wei H B, et al. Molecular phylogeny of coronaviruses including human SARS-CoV. Chinese Sci Bull, 2003, 48: 1170-1174.
    • (2003) Chinese Sci Bull , vol.48 , pp. 1170-1174
    • Gao, L.1    Qi, J.2    Wei, H.B.3
  • 8
    • 34047110724 scopus 로고    scopus 로고
    • Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
    • Gao L, Qi J. Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol Biol, 2007, 7: 41, doi: 10. 1086/1471-2148/7/41.
    • (2007) BMC Evol Biol , vol.7 , pp. 41
    • Gao, L.1    Qi, J.2
  • 9
    • 33646797802 scopus 로고    scopus 로고
    • Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes
    • Chu K H, Qi J, Yu Z G, et al. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol, 2004, 28: 70-76.
    • (2004) Mol Biol Evol , vol.28 , pp. 70-76
    • Chu, K.H.1    Qi, J.2    Yu, Z.G.3
  • 10
    • 34648815169 scopus 로고    scopus 로고
    • Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology
    • Gao L, Qi J, Sun J D, et al. Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology. Sci China Ser C-Life Sci, 2007, 50: 587-599.
    • (2007) Sci China Ser C-Life Sci , vol.50 , pp. 587-599
    • Gao, L.1    Qi, J.2    Sun, J.D.3
  • 11
    • 69949152972 scopus 로고    scopus 로고
    • A fungal phylogeny based on 82 complete genomes using the composition vector method
    • Wang H, Xu Z, Hao B L. A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol Biol, 2009, 9: 195, doi: 10. 1186/1471-2148-9-195.
    • (2009) BMC Evol Biol , vol.9 , pp. 195
    • Wang, H.1    Xu, Z.2    Hao, B.L.3
  • 12
    • 84874667657 scopus 로고    scopus 로고
    • NCBI FTP site: ftp://ftp. ncbi. nih. gov/genomes/Bacteria/.
    • NCBI FTP site
  • 13
    • 52149085893 scopus 로고    scopus 로고
    • The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains
    • Yarza P, Richter M, Peplies J, et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. System Appl Microbiol, 2008, 31: 241-250.
    • (2008) System Appl Microbiol , vol.31 , pp. 241-250
    • Yarza, P.1    Richter, M.2    Peplies, J.3
  • 14
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic tress
    • Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic tress. Mol Biol Evol, 1987, 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 16
    • 3242890106 scopus 로고    scopus 로고
    • CVTree: A phylogenetic tree reconstruction tool based on whole genomes
    • Qi J, Luo H, Hao B L. CVTree: A phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res, 2004, 32, Web Server Issue: W45-W47.
    • (2004) Nucleic Acids Res , vol.32 , Issue.WebServerIssue
    • Qi, J.1    Luo, H.2    Hao, B.L.3
  • 17
    • 67849101838 scopus 로고    scopus 로고
    • Xu Z, Hao B L. CVTree update: A phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res, 2009, doi: 10. 1093/ nar/gkp278.
  • 19
    • 33746531322 scopus 로고    scopus 로고
    • Genome of Rice Cluster I archaea - The key methane producers in the rice rhizospere
    • Erkel C, Kube M, Reinhardt R, et al. Genome of Rice Cluster I archaea - The key methane producers in the rice rhizospere. Science, 2006, 313: 370-372.
    • (2006) Science , vol.313 , pp. 370-372
    • Erkel, C.1    Kube, M.2    Reinhardt, R.3
  • 21
    • 0242300069 scopus 로고    scopus 로고
    • The genome of nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
    • Waters E, Hohn M J, Ahel I, et al. The genome of nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA, 2003, 100: 12984-12988.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 12984-12988
    • Waters, E.1    Hohn, M.J.2    Ahel, I.3
  • 22
    • 33751258603 scopus 로고    scopus 로고
    • The bacterial species dilemma and the genomic-phylogenetic species concept
    • Staley J T. The bacterial species dilemma and the genomic-phylogenetic species concept. Phil Trans R Soc, B, 2006, 361: 1899-1909.
    • (2006) Phil Trans R Soc, B , vol.361 , pp. 1899-1909
    • Staley, J.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.