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It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.

Titel:	Discordant phylogenies within the rrn loci of Rhizobia.
Autor/in / Beteiligte Person:	van Berkum P ; Terefework, Z ; Paulin, L ; Suomalainen, S ; Lindström, K ; Eardly, BD
Link:	Full Text Finder (Volltext)
Zeitschrift:	Journal of bacteriology, Jg. 185 (2003-05-01), Heft 10, S. 2988-98
Veröffentlichung:	Washington, DC : American Society for Microbiology, 2003
Medientyp:	academicJournal
ISSN:	0021-9193 (print)
DOI:	10.1128/JB.185.10.2988-2998.2003
Schlagwort:	Base Sequence Evolution, Molecular Gene Conversion Likelihood Functions Molecular Sequence Data Polymerase Chain Reaction methods Polymorphism, Genetic Recombination, Genetic Rhizobiaceae physiology Sequence Homology, Nucleic Acid DNA, Intergenic Phylogeny RNA, Ribosomal, 16S RNA, Ribosomal, 23S Rhizobiaceae genetics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Comment; Journal Article Language: English [J Bacteriol] 2003 May; Vol. 185 (10), pp. 2988-98. MeSH Terms: DNA, Intergenic* ; Phylogeny* ; RNA, Ribosomal, 16S* ; RNA, Ribosomal, 23S* ; Rhizobiaceae / *genetics ; Base Sequence ; Evolution, Molecular ; Gene Conversion ; Likelihood Functions ; Molecular Sequence Data ; Polymerase Chain Reaction / methods ; Polymorphism, Genetic ; Recombination, Genetic ; Rhizobiaceae / physiology ; Sequence Homology, Nucleic Acid Comments: Comment on: J Bacteriol. 2003 May;185(10):2975-9. (PMID: 12730155) References: J Mol Biol. 1970 Apr 28;49(2):297-317. (PMID: 5447822) ; Genome Res. 2000 Nov;10(11):1719-25. (PMID: 11076857) ; Science. 1997 Sep 5;277(5331):1453-62. (PMID: 9278503) ; Curr Opin Genet Dev. 2000 Dec;10(6):606-11. (PMID: 11088009) ; Int J Syst Evol Microbiol. 2001 Nov;51(Pt 6):2037-2048. (PMID: 11760945) ; Appl Environ Microbiol. 1993 Dec;59(12):4161-5. (PMID: 16349115) ; Curr Biol. 1999 Oct 7;9(19):R747-51. (PMID: 10531001) ; Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12381-5. (PMID: 9770495) ; J Bacteriol. 1994 Feb;176(4):1121-7. (PMID: 8106323) ; Appl Microbiol. 1955 Nov;3(6):361-8. (PMID: 13269089) ; J Bacteriol. 1997 Jun;179(11):3736-45. (PMID: 9171424) ; Int J Syst Evol Microbiol. 2001 Jan;51(Pt 1):111-7. (PMID: 11211247) ; Annu Rev Microbiol. 2001;55:709-42. (PMID: 11544372) ; Genome Res. 2001 May;11(5):731-53. (PMID: 11337471) ; Int J Syst Bacteriol. 1996 Jan;46(1):240-4. (PMID: 8573502) ; Trends Microbiol. 2002 Feb;10(2):94-9. (PMID: 11827811) ; Int J Syst Bacteriol. 1993 Jul;43(3):626-9. (PMID: 8347521) ; Extremophiles. 2000 Dec;4(6):373-6. (PMID: 11139080) ; J Bacteriol. 2001 Jan;183(1):214-20. (PMID: 11114919) ; Lett Appl Microbiol. 1995 Dec;21(6):402-5. (PMID: 8554768) ; Curr Opin Genet Dev. 2001 Dec;11(6):620-6. (PMID: 11682304) ; Appl Environ Microbiol. 1990 Dec;56(12):3835-41. (PMID: 16348383) ; Gene. 1996 Oct 31;178(1-2):15-23. (PMID: 8921885) ; J Bacteriol. 1999 Sep;181(17):5201-9. (PMID: 10464188) ; Nucleic Acids Res. 1990 Dec 25;18(24):7267-77. (PMID: 1701878) ; Syst Biol. 2000 Dec;49(4):652-70. (PMID: 12116432) ; J Bacteriol. 1994 Jan;176(1):1-6. (PMID: 8282683) ; J Mol Evol. 1989 Aug;29(2):170-9. (PMID: 2509717) ; Mol Biol Evol. 1996 Mar;13(3):451-61. (PMID: 8742634) ; EMBO J. 1992 Apr;11(4):1309-16. (PMID: 1339343) ; Int J Syst Evol Microbiol. 2000 Nov;50 Pt 6:2165-2172. (PMID: 11155993) ; Appl Environ Microbiol. 2002 Mar;68(3):1132-6. (PMID: 11872460) ; Microbiology (Reading). 1994 Nov;140 ( Pt 11):3053-60. (PMID: 7812446) ; Plant Mol Biol. 1997 Dec;35(6):873-92. (PMID: 9426607) ; Nature. 2002 Jan 31;415(6871):497-502. (PMID: 11823852) ; Nature. 2001 Jan 25;409(6819):529-33. (PMID: 11206551) ; J Gen Microbiol. 1965 Jun;39(3):311-20. (PMID: 5324933) ; Res Microbiol. 2001 Jun;152(5):421-30. (PMID: 11446510) ; Nature. 2000 Jul 13;406(6792):151-9. (PMID: 10910347) ; Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9413-7. (PMID: 9689094) ; Lancet. 2001 Apr 21;357(9264):1225-40. (PMID: 11418146) ; Appl Environ Microbiol. 1997 Jun;63(6):2330-7. (PMID: 9172352) ; Cell Mol Life Sci. 1999 Nov 30;56(9-10):755-63. (PMID: 11212335) ; Science. 2000 Mar 10;287(5459):1809-15. (PMID: 10710307) ; Proc Natl Acad Sci U S A. 1994 Oct 11;91(21):10227-31. (PMID: 7937867) ; Nature. 1997 Nov 20;390(6657):249-56. (PMID: 9384377) ; Int J Syst Bacteriol. 1998 Oct;48 Pt 4:1277-90. (PMID: 9828428) ; Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4658-63. (PMID: 11296296) ; Int J Syst Evol Microbiol. 2001 Jan;51(Pt 1):89-103. (PMID: 11211278) ; Microbiology (Reading). 1999 Aug;145 ( Pt 8):2095-2103. (PMID: 10463176) ; J Bacteriol. 1979 Sep;139(3):842-9. (PMID: 383696) ; J Bacteriol. 1995 Dec;177(23):6993-8. (PMID: 7592497) ; Nature. 2000 Sep 28;407(6803):508-13. (PMID: 11029001) ; EMBO J. 1992 Nov;11(11):4175-85. (PMID: 1396599) ; Microbiology (Reading). 1996 Aug;142 ( Pt 8):2087-95. (PMID: 8760921) ; Nature. 2001 Jun 21;411(6840):948-50. (PMID: 11418858) ; J Mol Evol. 1997 Apr;44(4):383-97. (PMID: 9089078) ; Nature. 1999 May 27;399(6734):323-9. (PMID: 10360571) ; Nature. 2000 May 18;405(6784):299-304. (PMID: 10830951) ; Biochem J. 1975 Jul;149(1):17-22. (PMID: 1191256) ; Microbiology (Reading). 2000 Nov;146 ( Pt 11):2845-2854. (PMID: 11065363) ; Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):1033-7. (PMID: 8430070) ; J Bacteriol. 1997 May;179(10):3270-6. (PMID: 9150223) Substance Nomenclature: 0 (DNA, Intergenic) ; 0 (RNA, Ribosomal, 16S) ; 0 (RNA, Ribosomal, 23S) Entry Date(s): Date Created: 20030506 Date Completed: 20030616 Latest Revision: 20240322 Update Code: 20240322 PubMed Central ID: PMC154066

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Discordant phylogenies within the rrn loci of Rhizobia.