|
|
||||||||
The FASEB Journal, Vol 7, 113-123, Copyright © 1993 by The Federation of American Societies for Experimental Biology
REVIEWS |
GJ Olsen and CR Woese
Department of Microbiology, University of Illinois, Urbana 61801.
As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.
This article has been cited by other articles:
![]() |
J. R. Zaneveld, C. Lozupone, J. I. Gordon, and R. Knight Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives Nucleic Acids Res., March 2, 2010; (2010) gkq066v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. T. Montone Differentiation of Fusarium From Aspergillus Species by Colorimetric In Situ Hybridization in Formalin-Fixed, Paraffin-Embedded Tissue Sections Using Dual Fluorogenic-Labeled LNA Probes Am J Clin Pathol, December 1, 2009; 132(6): 866 - 870. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Menna, F. G. Barcellos, and M. Hungria Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes Int J Syst Evol Microbiol, December 1, 2009; 59(12): 2934 - 2950. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. S. Gupta Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2510 - 2526. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Alexandre, M. Laranjo, J. P. W. Young, and S. Oliveira dnaJ is a useful phylogenetic marker for alphaproteobacteria Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2839 - 2849. [Abstract] [Full Text] [PDF] |
||||
![]() |
V. Bouchet, H. Huot, and R. Goldstein Molecular Genetic Basis of Ribotyping Clin. Microbiol. Rev., April 1, 2008; 21(2): 262 - 273. [Abstract] [Full Text] [PDF] |
||||
![]() |
V. Gowri-Shankar and M. Rattray A Reversible Jump Method for Bayesian Phylogenetic Inference with a Nonhomogeneous Substitution Model Mol. Biol. Evol., June 1, 2007; 24(6): 1286 - 1299. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C Y Woo, L. M W Chung, J. L L Teng, H. Tse, S. S Y Pang, V. Y T Lau, V. W K Wong, K.-l. Kam, S. K P Lau, and K.-Y. Yuen In silico analysis of 16S ribosomal RNA gene sequencing-based methods for identification of medically important anaerobic bacteria J. Clin. Pathol., May 1, 2007; 60(5): 576 - 579. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Martens, M. Delaere, R. Coopman, P. De Vos, M. Gillis, and A. Willems Multilocus sequence analysis of Ensifer and related taxa Int J Syst Evol Microbiol, March 1, 2007; 57(3): 489 - 503. [Abstract] [Full Text] [PDF] |
||||
![]() |
X.-P. Ni, S.-H. Ren, J.-R. Sun, H.-Q. Xiang, Y. Gao, Q.-X. Kong, J. Cha, J.-C. Pan, H. Yu, and H.-M. Li Laribacter hongkongensis Isolated from a Patient with Community-Acquired Gastroenteritis in Hangzhou City J. Clin. Microbiol., January 1, 2007; 45(1): 255 - 256. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. F. Mazzeo, A. Sorrentino, M. Gaita, G. Cacace, M. Di Stasio, A. Facchiano, G. Comi, A. Malorni, and R. A. Siciliano Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Discrimination of Food-Borne Microorganisms Appl. Envir. Microbiol., February 1, 2006; 72(2): 1180 - 1189. [Abstract] [Full Text] [PDF] |
||||
![]() |
S K P Lau, K H L Ng, P C Y Woo, K-t Yip, A M Y Fung, G K S Woo, K-m Chan, T-l Que, and K-y Yuen Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic Gram positive bacilli isolated from blood cultures J. Clin. Pathol., February 1, 2006; 59(2): 219 - 222. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. G. Germano, P. Menna, F. L. Mostasso, and M. Hungria RFLP analysis of the rRNA operon of a Brazilian collection of bradyrhizobial strains from 33 legume species Int J Syst Evol Microbiol, January 1, 2006; 56(1): 217 - 229. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Zhao, R. E. Davis, and I.-M. Lee Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins Int J Syst Evol Microbiol, September 1, 2005; 55(5): 2131 - 2141. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Bardeleben, R. L. Moore, and R. K. Wayne Isolation and Molecular Evolution of the Selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) Genes in the Dog Family, Canidae Mol. Biol. Evol., February 1, 2005; 22(2): 347 - 359. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. S. Jermiin, S. Y.W. Ho, F. Ababneh, J. Robinson, and A. W.D. Larkum The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated Syst Biol, August 1, 2004; 53(4): 638 - 643. [Full Text] [PDF] |
||||
![]() |
S. K. P. Lau, P. C. Y. Woo, M.-y. Mok, J. L. L. Teng, V. K. P. Tam, K. K. H. Chan, and K.-y. Yuen Characterization of Haemophilus segnis, an Important Cause of Bacteremia, by 16S rRNA Gene Sequencing J. Clin. Microbiol., February 1, 2004; 42(2): 877 - 880. [Abstract] [Full Text] [PDF] |
||||
![]() |
P C Y Woo, S K P Lau, A M Y Fung, S K Chiu, R W H Yung, and K Y Yuen Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing J. Clin. Pathol., September 1, 2003; 56(9): 690 - 693. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, K. H. L. Ng, S. K. P. Lau, K.-t. Yip, A. M. Y. Fung, K.-w. Leung, D. M. W. Tam, T.-l. Que, and K.-y. Yuen Usefulness of the MicroSeq 500 16S Ribosomal DNA-Based Bacterial Identification System for Identification of Clinically Significant Bacterial Isolates with Ambiguous Biochemical Profiles J. Clin. Microbiol., May 1, 2003; 41(5): 1996 - 2001. [Abstract] [Full Text] [PDF] |
||||
![]() |
A.-V. Taillardat-Bisch, D. Raoult, and M. Drancourt RNA polymerase {beta}-subunit-based phylogeny of Ehrlichia spp., Anaplasma spp., Neorickettsia spp. and Wolbachia pipientis Int J Syst Evol Microbiol, March 1, 2003; 53(2): 455 - 458. [Abstract] [Full Text] [PDF] |
||||
![]() |
J L L Teng, P C Y Woo, K W Leung, S K P Lau, M K M Wong, and K Y Yuen Pseudobacteraemia in a patient with neutropenic fever caused by a novel paenibacillus species: Paenibacillus hongkongensis sp. nov. Mol. Pathol., February 1, 2003; 56(1): 29 - 35. [Abstract] [Full Text] [PDF] |
||||
![]() |
Z. Zeaiter, Z. Liang, and D. Raoult Genetic Classification and Differentiation of Bartonella Species Based on Comparison of Partial ftsZ Gene Sequences J. Clin. Microbiol., October 1, 2002; 40(10): 3641 - 3647. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Grande, J. Templado, J. Lucas Cervera, and R. Zardoya The Complete Mitochondrial Genome of the Nudibranch Roboastra europaea (Mollusca: Gastropoda) Supports the Monophyly of Opisthobranchs Mol. Biol. Evol., October 1, 2002; 19(10): 1672 - 1685. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. G. Lawrence, G. F. Hatfull, and R. W. Hendrix Imbroglios of Viral Taxonomy: Genetic Exchange and Failings of Phenetic Approaches J. Bacteriol., September 1, 2002; 184(17): 4891 - 4905. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C.-Y. WOO, K.-W. LEUNG, H.-W. TSOI, S. S.-Y. WONG, J. L.-L. TENG, and K.-Y. YUEN Thermo-tolerant Campylobacter fetus bacteraemia identified by 16S ribosomal RNA gene sequencing: an emerging pathogen in immunocompromised patients J. Med. Microbiol., September 1, 2002; 51(9): 740 - 746. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. K.-P. LAU, P. C.-Y. WOO, B. Y.-L. CHAN, A. M.-Y. FUNG, T.-L. QUE, and K.-Y. YUEN Haemophilus segnis polymicrobial and monomicrobial bacteraemia identified by 16S ribosomal RNA gene sequencing J. Med. Microbiol., August 1, 2002; 51(8): 635 - 640. [Abstract] [Full Text] [PDF] |
||||
![]() |
S K P Lau, P C Y Woo, J L L Teng, K W Leung, and K Y Yuen Identification by 16S ribosomal RNA gene sequencing of Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis Mol. Pathol., June 1, 2002; 55(3): 182 - 185. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, K.-W. Leung, S. S. Y. Wong, K. T. K. Chong, E. Y. L. Cheung, and K.-Y. Yuen Relatively Alcohol-Resistant Mycobacteria Are Emerging Pathogens in Patients Receiving Acupuncture Treatment J. Clin. Microbiol., April 1, 2002; 40(4): 1219 - 1224. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. M. Simpson, S. A. Kocherginskaya, R. I. Aminov, L. T. Skerlos, T. M. Bradley, R. I. Mackie, and B. A. White Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species Integr. Comp. Biol., April 1, 2002; 42(2): 327 - 331. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, D. M. W. Tam, K.-W. Leung, S. K. P. Lau, J. L. L. Teng, M. K. M. Wong, and K.-Y. Yuen Streptococcus sinensis sp. nov., a Novel Species Isolated from a Patient with Infective Endocarditis J. Clin. Microbiol., March 1, 2002; 40(3): 805 - 810. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, A. M. Y. Fung, S. K. P. Lau, and K.-Y. Yuen Identification by 16S rRNA Gene Sequencing of Lactobacillus salivarius Bacteremic Cholecystitis J. Clin. Microbiol., January 1, 2002; 40(1): 265 - 267. [Abstract] [Full Text] [PDF] |
||||
![]() |
K.-Y. Yuen, P. C. Y. Woo, J. L. L. Teng, K.-W. Leung, M. K. M. Wong, and S. K. P. Lau Laribacterhongkongensis gen. nov., sp. nov., a Novel Gram-Negative Bacterium Isolated from a Cirrhotic Patient with Bacteremia and Empyema J. Clin. Microbiol., December 1, 2001; 39(12): 4227 - 4232. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. J. Laamanen, M. F. Gugger, J. M. Lehtimaki, K. Haukka, and K. Sivonen Diversity of Toxic and Nontoxic Nodularia Isolates (Cyanobacteria) and Filaments from the Baltic Sea Appl. Envir. Microbiol., October 1, 2001; 67(10): 4638 - 4647. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, A. M. Y. Fung, S. K. P. Lau, S. S. Y. Wong, and K.-Y. Yuen Group G Beta-Hemolytic Streptococcal Bacteremia Characterized by 16S Ribosomal RNA Gene Sequencing J. Clin. Microbiol., September 1, 2001; 39(9): 3147 - 3155. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. J. Rolph, A. Lennon, M. P. Riggio, W. P. Saunders, D. MacKenzie, L. Coldero, and J. Bagg Molecular Identification of Microorganisms from Endodontic Infections J. Clin. Microbiol., September 1, 2001; 39(9): 3282 - 3289. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Griffiths and R. S. Gupta The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division Microbiology, September 1, 2001; 147(9): 2611 - 2622. [Abstract] [Full Text] [PDF] |
||||
![]() |
P C Y Woo, A S P Leung, K W Leung, and K Y Yuen Identification of slide coagulase positive, tube coagulase negative Staphylococcus aureus by 16S ribosomal RNA gene sequencing Mol. Pathol., August 1, 2001; 54(4): 244 - 247. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Drancourt, A. Carlioz, and D. Raoult rpoB Sequence Analysis of Cultured Tropheryma whippelii J. Clin. Microbiol., July 1, 2001; 39(7): 2425 - 2430. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Barloy-Hubler, V. Lelaure, and F. Galibert Ribosomal protein gene cluster analysis in eubacterium genomics: homology between Sinorhizobium meliloti strain 1021 and Bacillus subtilis Nucleic Acids Res., July 1, 2001; 29(13): 2747 - 2756. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Sanchis, J. M. Michelena, A. Latorre, D. L. J. Quicke, U. Gardenfors, and R. Belshaw The Phylogenetic Analysis of Variable-Length Sequence Data: Elongation Factor-1{{alpha}} Introns in European Populations of the Parasitoid Wasp Genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) Mol. Biol. Evol., June 1, 2001; 18(6): 1117 - 1131. [Abstract] [Full Text] |
||||
![]() |
R. Zardoya and A. Meyer On the origin of and phylogenetic relationships among living amphibians PNAS, May 30, 2001; (2001) 111455498. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. S. Makarova, L. Aravind, Y. I. Wolf, R. L. Tatusov, K. W. Minton, E. V. Koonin, and M. J. Daly Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics Microbiol. Mol. Biol. Rev., March 1, 2001; 65(1): 44 - 79. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, A. M. Y. Fung, S. S. Y. Wong, H.-W. Tsoi, and K.-Y. Yuen Isolation and Characterization of a Salmonella enterica Serotype Typhi Variant and Its Clinical and Public Health Implications J. Clin. Microbiol., March 1, 2001; 39(3): 1190 - 1194. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. J. Savill, D. C. Hoyle, and P. G. Higgs RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods Genetics, January 1, 2001; 157(1): 399 - 411. [Abstract] [Full Text] |
||||
![]() |
N. B. Mugridge, D. A. Morrison, T. Jakel, A. R. Heckeroth, A. M. Tenter, and A. M. Johnson Effects of Sequence Alignment and Structural Domains of Ribosomal DNA on Phylogeny Reconstruction for the Protozoan Family Sarcocystidae Mol. Biol. Evol., December 1, 2000; 17(12): 1842 - 1853. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. C. Y. Woo, H.-W. Tsoi, K.-W. Leung, P. N. L. Lum, A. S. P. Leung, C.-H. Ma, K.-M. Kam, and K.-Y. Yuen Identification of Mycobacterium neoaurum Isolated from a Neutropenic Patient with Catheter-Related Bacteremia by 16S rRNA Sequencing J. Clin. Microbiol., September 1, 2000; 38(9): 3515 - 3517. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. E. M. Jaeger, N. M. Carroll, S. Choudhury, A. A. S. Dunlop, H. M. A. Towler, M. M. Matheson, P. Adamson, N. Okhravi, and S. Lightman Rapid Detection and Identification of Candida, Aspergillus, and Fusarium Species in Ocular Samples Using Nested PCR J. Clin. Microbiol., August 1, 2000; 38(8): 2902 - 2908. [Abstract] [Full Text] [PDF] |
||||
![]() |
P C Y Woo, P K L Leung, K W Leung, and K Y Yuen Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species from a bone marrow transplant recipient Mol. Pathol., August 1, 2000; 53(4): 211 - 215. [Abstract] [Full Text] |
||||
![]() |
R. Zardoya and A. Meyer Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona) Genetics, June 1, 2000; 155(2): 765 - 775. [Abstract] [Full Text] |
||||
![]() |
J. Castresana Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Mol. Biol. Evol., April 1, 2000; 17(4): 540 - 552. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Van de Peer, P. De Rijk, J. Wuyts, T. Winkelmans, and R. De Wachter The European Small Subunit Ribosomal RNA database Nucleic Acids Res., January 1, 2000; 28(1): 175 - 176. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. A. Herr, L. Ajello, J. W. Taylor, S. N. Arseculeratne, and L. Mendoza Phylogenetic Analysis of Rhinosporidium seeberi's 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade J. Clin. Microbiol., September 1, 1999; 37(9): 2750 - 2754. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. M. Olive and P. Bean Principles and Applications of Methods for DNA-Based Typing of Microbial Organisms J. Clin. Microbiol., June 1, 1999; 37(6): 1661 - 1669. [Full Text] [PDF] |
||||
![]() |
R. I Mackie, A. Sghir, and H R. Gaskins Developmental microbial ecology of the neonatal gastrointestinal tract Am. J. Clinical Nutrition, May 1, 1999; 69 (5): 1035S - 1045S. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Shi, W. W. Carmichael, and P. J. Kennelly Cyanobacterial PPP Family Protein Phosphatases Possess Multifunctional Capabilities and Are Resistant to Microcystin-LR J. Biol. Chem., April 9, 1999; 274(15): 10039 - 10046. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Franzen and A. Muller Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia Clin. Microbiol. Rev., April 1, 1999; 12(2): 243 - 285. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. W. Gray, G. Burger, and B. F. Lang Mitochondrial Evolution Science, March 5, 1999; 283(5407): 1476 - 1481. [Abstract] [Full Text] |
||||
![]() |
R. S. Gupta Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes Microbiol. Mol. Biol. Rev., December 1, 1998; 62(4): 1435 - 1491. [Abstract] [Full Text] [PDF] |
||||
![]() |
M J BLASER Helicobacters are indigenous to the human stomach: duodenal ulceration is due to changes in gastric microecology in the modern era Gut, November 1, 1998; 43(5): 721 - 727. [Full Text] [PDF] |
||||
![]() |
J. E. Barlough, G. H. Reubel, J. E. Madigan, L. K. Vredevoe, P. E. Miller, and Y. Rikihisa Detection of Ehrlichia risticii, the Agent of Potomac Horse Fever, in Freshwater Stream Snails (Pleuroceridae: Juga spp.) from Northern California Appl. Envir. Microbiol., August 1, 1998; 64(8): 2888 - 2893. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. R. M. Tillier and R. A. Collins High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA Genetics, April 1, 1998; 148(4): 1993 - 2002. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. Sullivan and D. Coleman Candida dubliniensis: Characteristics and Identification J. Clin. Microbiol., February 1, 1998; 36(2): 329 - 334. [Full Text] [PDF] |
||||
![]() |
J. J. Wernegreen, E. E. Harding, and M. A. Riley Rhizobium gone native: Unexpected plasmid stability of indigenous Rhizobium leguminosarum PNAS, May 13, 1997; 94(10): 5483 - 5488. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. L. True and D. W. Celander Ribonuclease P of Tetrahymena thermophila J. Biol. Chem., July 12, 1996; 271(28): 16559 - 16566. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Zardoya and A. Meyer On the origin of and phylogenetic relationships among living amphibians PNAS, June 19, 2001; 98(13): 7380 - 7383. [Abstract] [Full Text] [PDF] |
||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |