CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

Genomics, Proteomics and Bioinformatics

Volumn 13, Issue 5, 2015, Pages 321-331

  Zuo, Guanghong ^a   Hao, Bailin ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

Alignment free phylogeny; Archaea and Bacteria taxonomy; Composition vector; CVTree; Whole genome based tree

Indexed keywords

RNA 16S;

ALIGNMENT FREE PROKARYOTIC PHYLOGENY; ARTICLE; GENOME; NONHUMAN; PHYLOGENY; PROKARYOTE; SPECIES; TAXONOMIC RANK; TAXONOMY; ARCHAEAL GENOME; ARCHAEON; BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; GENETICS; INTERNET; PROCEDURES; RETROSPECTIVE STUDY; SEQUENCE ALIGNMENT;

ARCHAEA; BACTERIA; GENOME, ARCHAEAL; GENOME, BACTERIAL; INTERNET; PHYLOGENY; RETROSPECTIVE STUDIES; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT;

EID: 84949446800     PISSN: 16720229     EISSN: 22103244     Source Type: Journal    
DOI: 10.1016/j.gpb.2015.08.004     Document Type: Article

References (67)

1. Whitman W.B., Coleman D.C., Wiebe W.J. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 1998, 95:6578-6583.
2. Fox G.E., Pechman K.R., Woese C.R. Comparative cataloging of 16S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. Int J Syst Bacteriol 1977, 27:44-57.
3. Bergey's Manual Trust. Bergey's manual of systematic bacteriology, 2nd ed., vol 1-5. New York: Springer-Verlag; 2001-2012.
4. Woese C.R., Stackebrandt E., Macke T.J., Fox G.E. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985, 6:143-151.
5. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987, 37:463-464.
6. Coneye T., Gevers D., Van der Peer Y., Vandamme P., Swings J. Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 2005, 29:147-167.
7. Konstandinidis K.T., Tiedje J.M. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005, 187:6258-6264.
8. Klenk H.P., Goker M. En route to a genome-based classification of Archaea and Bacteria. Syst Appl Microbiol 2010, 33:175-182.
9. Jun S.R., Sims G.E., Wu G.A., Kim S.H. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. Proc Natl Acad Sci U S A 2010, 107:133-138.
10. Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014, 64:316-324.
11. Wu D., Hugenholtz P., Mavromtis K., Pukall R., Dalin E., Ivanova N.N., et al. A phylogeny-driven encyclopedia of Bacteria and Archaea. Nature 2009, 462:1056-1060.
12. Kyrpides N.C., Hugenholtz P., Eisen J.A., Woyke T., Göker M., Parker C.T., et al. Genomic encyclopedia of Bacteria and Archaea: sequencing a myriad of type strains. PLoS Biol 2014, 12:e1001920.
13. Qi J., Wang B., Hao B.L. Whole genome prokaryote phylogeny without sequence alignment: a K-string composition vector approach. J Mol Evol 2004, 58:1-11.
14. Hao B.L., Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J Bioinform Comput Biol 2004, 2:1-19.
15. Gao L., Qi J., Sun J.D., Hao B.L. Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology. Sci China C Life Sci 2007, 50:587-599.
16. Li Q., Xu Z., Hao B.L. Composition vector approach to whole genome-based prokaryote phylogeny: success and foundations. J Biotechnol 2010, 149:115-119.
17. Hao B.L. Whole-genome based prokaryotic branches of the tree of life. Darwin's heritage today: Proceedings of the Darwin 200 Beijing International Conference 2010, 101-113. High Education Press, Beijing. M. Long, G. Hongya, Z. Zhou (Eds.).
18. Sun J.D., Xu Z., Hao B.L. Whole-genome based Archaea phylogeny and taxonomy - a composition vector approach. Chin Sci Bull 2010, 55:2323-2328.
19. Zuo G.H., Xu Z., Yu H.J., Hao B.L. Jackknife and bootstrap tests of the composition vector trees. Genomics Proteomics Bioinformatics 2010, 8:262-267.
20. Hao B.L. CVTrees support the Bergey's systematics and provide high resolution at species level and below. Bull BISMiS 2011, 2(Part 2):189-196.
21. Zuo G.H., Xu Z., Hao B.L. Shigella species are not strains of Escherichia coli but sister members in the genus Escherichia. Genomics Proteomics Bioinformatics 2013, 11:61-65.
22. Zuo G.H., Hao B.L., Staley J.T. Geographic divergence of 'Sulfolobus islandicus' strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars. Antonie van Leeuwenhoek 2014, 105:431-435.
23. Zuo G.H., Li Q., Hao B.L. On K-peptide length in composition vector phylogeny of prokaryotes. Comput Biol Chem 2014, 53:166-173.
24. Zuo G.H., Xu Z., Hao B.L. Phylogeny and taxonomy of Archaea: a comparison of the whole-genome-based CVTree approach with 16S rRNA sequence analysis. Life 2015, 5:949-968.
25. Chan R.H., Chan T.H., Yeung H.M., Wang R.W. Composition vector method based on maximal entropy principle for sequence comparison. IEEE/ACM Trans Comput Biol Bioinform 2012, 9:79-87.
26. Song K., Ren J., Reinert G., Deng M.H., Waterman M.S., Sun F.Z. New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief Bioinform 2013, 15:343-353.
27. Qi J., Luo H., Hao B.L. CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 2004, 32:W45-W47.
28. Xu Z., Hao B.L. CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucleic Acids Res 2009, 37:W174-W178.
29. Farris J.S. Formal definitions of paraphyly and monophyly. Syst Zool 1974, 23:548-554.
30. Farris J.S. Haeckel, history, and hull. Syst Zool 1990, 39:81-88.
31. Rinke C., Schwientek P., Sczybra A., Ivanova N.N., Anderson I.J., Cheng J.-F., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013, 499:431-437.
32. Giongo A., Tyler H.L., Zipperer U.N., Triplett E.W. Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PIA 5, suggest a new standard in genome sequence submission. Stand Genomic Sci 2010, 2:309-317.
33. Gao L., Qi J., Wei H.B., Sun Y.G., Hao B.L. Molecular phylogeny of coronaviruses including human SARS-CoV. Chin Sci Bull 2003, 48:1170-1174.
34. Gao L., Qi J. Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol Biol 2007, 7:41.
35. Chu K.S., Qi J., Yu Z.G., Ahn V. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol 2004, 28:70-76.
36. Wang H., Xu Z., Gao L., Hao B.L. A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol Biol 2009, 9:195.
37. Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 1977, 74:5088-5090.
38. Garrity G.M., Johnson K.L., Lilburn T.G. Taxonomic outline of the procaryotes. Bergey's manual of systematic bacteriology, Rel. 3.0 2002, Springer, New York. 2nd ed., 10.1007/bergeysoutline200210.
39. Garrity G.M., Bell J.A., Lilburn T.G. Taxonomic outline of the procaryotes. Bergey's manual of systematic bacteriology, Rel. 4.0 2003, Springer, New York. 2nd ed., 10.1007/bergeysoutline200310.
40. Garrity G.M., Bell J.A., Lilburn T.G. Taxonomic outline of the procaryotes. Bergey's manual of systematic bacteriology, Rel. 5.0 2004, Springer, New York. 2nd ed., 10.1007/bergeysoutline200405.
41. Takai K., Suzuki M., Nakagawa S., Miyazaki M., Suzuki Y., Inagaki F., et al. Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2006, 56:1725-1738.
42. Fardeau M.-L., Bonilla-Salinas M., L'Haridon S., Jeanthon C., Verhe F., Cayol J.-L., et al. Isolation from oil reservoirs of novel thermophilic anaerobes phylogenetically related to Thermoanaerobacter subterraneus: reassignment of T. subterraneus, Thermoanaerobacter yonseiensis, Thermoanaerobacter tengcongensis and Carboxydibrachium pacificum to Caldanaerobacter subterraneus gen. nov., sp. nov., comb. nov. as four novel subspecies. Int J Syst Evol Microbiol 2004, 54:467-474.
43. Hugenholtz P., Stackebrandt E. Reclassification of Sphaerobacter thermophiles from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia in the phylum Chloroflexi. Int J Syst Evol Microbiol 2004, 54:2045-2051.
44. Iverson C., Mullane N., McCardell B., Tall B.D., Lehner A., Fanning S., et al. Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. Dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov. Int J Syst Evol Microbiol 2008, 56:1442-1447.
45. Liu C., Finegold S.M., Song Y., Lwson P.A. Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia productus comb. nov., Blautia schinkii comb. nov., and description of Blautia wexlerae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2008, 58:1896-1902.
46. Korczak B.M., Kuhnert P. Phylogeny of pasteurellaceae. Pasteurellaceae biology, genomics and molecular aspects 2008, 27-52. Caister Academic, Norwich, UK. P. Kuhnert, H. Christensen (Eds.).
47. Kuhnert P., Schalten E., Haefner S., Mayor D., Frey J. Basfia succiniciproducens gen. nov., sp. nov., a new member of the family Pasteurellaceae isolated from bovine rumen. Int J Syst Evol Microbiol 2010, 60:44-50.
48. Klenk H.-P., Lapidus A., Chertkov O., Copeland A., Del Rio T.G., Nolan M. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey 2010. Stand Genomic Sci 2011, 5:121-134.
49. Kunisawa T. The phylogenetic placement of he non-phototrophic, Gram-positive thermophile 'Thermobaculum terrenum' and branching orders within the phylum 'Chloroflexi' inferred from gene order comparisons. Int J Syst Evol Microbiol 2011, 61:1944-1953.
50. Yutin N., Galperin M.Y. A genomic update on clostridial phylogeny: Gram-negative spora formers and other misplaced clostridia. Environ Microbiol 2013, 15:2631-2641.
51. Parte A.C. LPSN - List of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014, 42:D613-D616.
52. Ramirez-Bahena M.-H., Chahboune R., Peix A., Velazquer E. Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov. Int J Syst Evol Microbiol 2013, 63:1013-1016.
53. Chan P.P., Cozen A.E., Lowe T.M. Reclassification of Thermoproteus neutrophilus Stetter and Zilling 1989 as Pyrobaculum neutrophilum comb. nov. based on phylogenetic analysis. Int J Syst Evol Microbiol 2013, 63:751-764.
54. Sen A., Daubin V., Abrouk D., Gifford I., Berry A.M., Normand P. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales' should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord nov. Int J Syst Evol Microbiol 2014, 64:3821-3832.
55. Gupta R.S., Naushad S., Baker S. Phylogenetic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobaceria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov. Int J Syst Evol Microbiol 2015, 65:1050-1069.
56. Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002, 52:7-76.
57. Lapage S.P., Sneath P.H.A., Lessel E.F., Skerman V.B.D., Seeliger H.P.R., Clark W.A. International Code of Nomenclature of Bacteria. Bacterial Code 1990 1992, ASM Press, Washington, DC.
58. Bhatnagar S., Badar J.H., Madupu R., Khouri H.M., O'Oconnor Y., Robb F.T., et al. Genome sequence of the sulfate-reducing thermophilic bacterium Thermodesulfovibrio yellowstonii strain DSM 11347T (phylum Nitrospirae). Genome Announc 2015, 3:e01489-e01514.
59. Collins M.D., Lawson P.A., Willems A., Cordoba J.J., Fernandez-Garayzabal J., Garcia P., et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994, 44:812-826.
60. Schloss P.D., Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev 2004, 68:686-691.
61. Löffler F.E., Yan J., Ritalahti K.M., Adrian L., Edwards E.A., Konstantinidis K.T., Muller J.A., et al. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 2013, 63:625-635.
62. Bazylinski D.A., Williams T.J., Lefevre C.T., Berg R.J., Zhang C.L., Bowser S.S., et al. Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria. Int J Syst Evol Microbiol 2013, 63:801-808.
63. Selander R.K., Caugant D.A., Whitman T.S. Genetic structure and variation in natural populations of Escherichia coli. Escherichia coli and Salmonella typhimurium. Cellular and molecular biology 1987, 1625-1647. American Society for Microbiology, Washington, DC. C. Niedhardt (Ed.).
64. Tenaillon O., Skurnik D., Picard B., Denamur E. The population genetics of commensal Escherichia coli. Nature Rev Microbiol 2010, 8:207-217.
65. Curtis T.P., Sloan W.T., Scannell J.W. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 2002, 99:10494-10499.
66. Whitman W.B. Intent of the nomenclatural Code and recommendations about naming new species based on genomic sequences. Bulletin BISMiS 2011, 2(Part 2):135-139.
67. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K.-H., et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008, 31:241-250.