Genome-based phylogenetic analysis of Streptomyces and its relatives

Molecular Phylogenetics and Evolution

Volumn 54, Issue 3, 2010, Pages 763-772

  Alam, Mohammad Tauqeer ^a   Merlo, Maria Elena ^a   Takano, Eriko ^a   Breitling, Rainer ^a  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Actinomycetales; Phylogeny; Rank order; rRNA; Streptomyces

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; GENE ORDER; GENETICS; GENOMICS; METHODOLOGY; PHYLOGENY; STREPTOMYCES;

GENE ORDER; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; PHYLOGENY; RNA, BACTERIAL; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA; STREPTOMYCES;

ACTINOMYCETALES; BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS; SALINISPORA TROPICA; STREPTOMYCES;

EID: 76449111368     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.11.019     Document Type: Article

References (54)

1. Anderson A.S., and Wellington E.M. The taxonomy of Streptomyces and related genera. Int. J. Syst. Evol. Microbiol. 51 (2001) 797-814
2. Barabote R.D., Xie G., Leu D.H., Normand P., Necsulea A., Daubin V., Medigue C., Adney W.S., Xu X.C., Lapidus A., Parales R.E., Detter C., Pujic P., Bruce D., Lavire C., Challacombe J.F., Brettin T.S., and Berry A.M. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res. 19 (2009) 1033-1043
3. Bentley S.D., Chater K.F., Cerdeno-Tarraga A.M., Challis G.L., Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.H., Kieser T., Larke L., Murphy L., Oliver K., O'Neil S., Rabbinowitsch E., Rajandream M.A., Rutherford K., Rutter S., Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A., Woodward J., Barrell B.G., Parkhill J., and Hopwood D.A. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417 (2002) 141-147
4. Borodina I., Krabben P., and Nielsen J. Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res. 15 (2005) 820-829
5. Breitling R., Armengaud P., Amtmann A., and Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 573 (2004) 83-92
6. Breitling R., Vitkup D., and Barrett M.P. New surveyor tools for charting microbial metabolic maps. Nat. Rev. Microbiol. 6 (2008) 156-161
7. Brown J.R., Douady C.J., Italia M.J., Marshall W.E., and Stanhope M.J. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28 (2001) 281-285
8. Casanova J.L., and Abel L. Genetic dissection of immunity to mycobacteria: the human model. Annu. Rev. Immunol. 20 (2002) 581-620
9. Castillo U.F., Strobel G.A., Ford E.J., Hess W.M., Porter H., Jensen J.B., Albert H., Robison R., Condron M.A., Teplow D.B., Stevens D., and Yaver D. Munumbicins, wide-spectrum antibiotics produced by Streptomyces NRRL 30562, endophytic on Kennedia nigriscans. Microbiology 148 (2002) 2675-2685
10. Cerdeno-Tarraga A.M., Efstratiou A., Dover L.G., Holden M.T., Pallen M., Bentley S.D., Besra G.S., Churcher C., James K.D., De Zoysa A., Chillingworth T., Cronin A., Dowd L., Feltwell T., Hamlin N., Holroyd S., Jagels K., Moule S., Quail M.A., Rabbinowitsch E., Rutherford K.M., Thomson N.R., Unwin L., Whitehead S., Barrell B.G., and Parkhill J. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 31 (2003) 6516-6523
11. Chater K.F., and Chandra G. The evolution of development in Streptomyces analysed by genome comparisons. FEMS Microbiol. Rev. 30 (2006) 651-672
12. Ciccarelli F.D., Doerks T., von Mering C., Creevey C.J., Snel B., and Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 311 (2006) 1283-1287
13. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry III C.E., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton J., Squares R., Squares S., Sulston J.E., Taylor K., Whitehead S., and Barrell B.G. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393 (1998) 537-544
14. Daubin V., Gouy M., and Perriere G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12 (2002) 1080-1090
15. Egan S., Wiener P., Kallifidas D., and Wellington E.M. Phylogeny of Streptomyces species and evidence for horizontal transfer of entire and partial antibiotic gene clusters. Antonie Van Leeuwenhoek 79 (2001) 127-133
16. Embley T.M., and Stackebrandt E. The molecular phylogeny and systematics of the actinomycetes. Annu. Rev. Microbiol. 48 (1994) 257-289
17. Felsenstein J. Phylogeny Inference Package Version 3.67 (2007), University of Washington, Seattle, WA pp. 98195-5065
18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
19. Fitch W.M., and Margoliash E. Construction of phylogenetic trees. Science 155 (1967) 279-284
20. Fitz-Gibbon S.T., and House C.H. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27 (1999) 4218-4222
21. Gao B., and Gupta R.S. Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int. J. Syst. Evol. Microbiol. 55 (2005) 2401-2412
22. Garrity, G.M., Bell, J.A., Lilburn, T.G., 2004. Taxonomic outline of the prokaryotes. In: Bergey's Manual of Systematic Bacteriology, second ed., release 5.0.
23. Goodfellow M., and Williams S.T. Ecology of actinomycetes. Annu. Rev. Microbiol. 37 (1983) 189-216
24. Henz S.R., Huson D.H., Auch A.F., Nieselt-Struwe K., and Schuster S.C. Whole-genome prokaryotic phylogeny. Bioinformatics 21 (2005) 2329-2335
25. Herniou E.A., Luque T., Chen X., Vlak J.M., Winstanley D., Cory J.S., and O'Reilly D.R. Use of whole genome sequence data to infer baculovirus phylogeny. J. Virol. 75 (2001) 8117-8126
26. Hopwood D.A. Streptomyces in Nature and Medicine: The Antibiotic Makers (2007), Oxford University Press
27. Huson D.H., and Steel M. Phylogenetic trees based on gene content. Bioinformatics 20 (2004) 2044-2049
28. Koonin E.V., Aravind L., and Kondrashov A.S. The impact of comparative genomics on our understanding of evolution. Cell 101 (2000) 573-576
29. Kost C., Lakatos T., Bottcher I., Arendholz W.R., Redenbach M., and Wirth R. Non-specific association between filamentous bacteria and fungus-growing ants. Naturwissenschaften 94 (2007) 821-828
30. Kunisawa T. Gene arrangements characteristic of the phylum Actinobacteria. Antonie Van Leeuwenhoek 92 (2007) 359-365
31. Lechevalier H.A., and Lechevalier M.P. Biology of actinomycetes. Annu. Rev. Microbiol. 21 (1967) 71-100
32. Lee S.D. Kineococcus marinus sp. nov., isolated from marine sediment of the coast of Jeju, Korea. Int. J. Syst. Evol. Microbiol. 56 (2006) 1279-1283
33. Leyden J.J. The evolving role of Propionibacterium acnes in acne. Semin. Cutan. Med. Surg. 20 (2001) 139-143
34. Lilburn T.G., and Garrity G.M. Exploring prokaryotic taxonomy. Int. J. Syst. Evol. Microbiol. 54 (2004) 7-13
35. Lin J., and Gerstein M. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 10 (2000) 808-818
36. Manteca A., Pelaez A.I., Zardoya R., and Sanchez J. Actinobacteria cyclophilins: phylogenetic relationships and description of new class- and order-specific paralogues. J. Mol. Evol. 63 (2006) 719-732
37. Montague M.G., and Hutchison III C.A. Gene content phylogeny of herpesviruses. Proc. Natl. Acad. Sci. USA 97 (2000) 5334-5339
38. Normand P., Lapierre P., Tisa L.S., Gogarten J.P., Alloisio N., Bagnarol E., Bassi C.A., Berry A.M., Bickhart D.M., Choisne N., Couloux A., Cournoyer B., Cruveiller S., Daubin V., Demange N., Francino M.P., Goltsman E., Huang Y., Kopp O.R., Labarre L., Lapidus A., Lavire C., Marechal J., Martinez M., Mastronunzio J.E., Mullin B.C., Niemann J., Pujic P., Rawnsley T., Rouy Z., Schenowitz C., Sellstedt A., Tavares F., Tomkins J.P., Vallenet D., Valverde C., Wall L.G., Wang Y., Medigue C., and Benson D.R. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res. 17 (2007) 7-15
39. Olsen G.J., and Woese C.R. Ribosomal RNA: a key to phylogeny. FASEB J. 7 (1993) 113-123
40. Phillips R.W., Wiegel J., Berry C.J., Fliermans C., Peacock A.D., White D.C., and Shimkets L.J. Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium. Int. J. Syst. Evol. Microbiol. 52 (2002) 933-938
41. Price N.D., Reed J.L., and Palsson B.O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol. 2 (2004) 886-897
42. Rokas A., and Holland P.W. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15 (2000) 454-459
43. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
44. Snel B., Bork P., and Huynen M.A. Genome phylogeny based on gene content. Nat. Genet. 21 (1999) 108-110
45. Snel B., Huynen M.A., and Dutilh B.E. Genome trees and the nature of genome evolution. Annu. Rev. Microbiol. 59 (2005) 191-209
46. Sourdis J., and Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol. Biol. Evol. 5 (1988) 298-311
47. Stackebrandt E., Rainey F.A., and Ward-Rainey N.L. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47 (1997) 479-491
48. Takeuchi T., Sawada H., Tanaka F., and Matsuda I. Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences. Int. J. Syst. Bacteriol. 46 (1996) 476-479
49. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
50. Tokala R.K., Strap J.L., Jung C.M., Crawford D.L., Salove M.H., Deobald L.A., Bailey J.F., and Morra M.J. Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum). Appl. Environ. Microbiol. 68 (2002) 2161-2171
51. Ventura M., Canchaya C., Tauch A., Chandra G., Fitzgerald G.F., Chater K.F., and van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 71 (2007) 495-548
52. Woese C.R. Bacterial evolution. Microbiol. Rev. 51 (1987) 221-271
53. Zhang H., Zhang W., Jin Y., Jin M., and Yu X. A comparative study on the phylogenetic diversity of culturable actinobacteria isolated from five marine sponge species. Antonie Van Leeuwenhoek 93 (2008) 241-248
54. Zhi X.Y., Li W.J., and Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int. J. Syst. Evol. Microbiol. 59 (2009) 589-608