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PMID: 12730157 Published · ppublish English Comment Journal Article

Discordant phylogenies within the rrn loci of Rhizobia.

Journal of bacteriology ·Vol. 185 ·No. 10 ·2003-05-00 ·Pages 2988-98

van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindström K, Eardly BD

Abstract

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.

MeSH Terms
Base Sequence DNA, Intergenic Evolution, Molecular Gene Conversion Likelihood Functions Molecular Sequence Data Phylogeny Polymerase Chain Reaction/methods Polymorphism, Genetic RNA, Ribosomal, 16S RNA, Ribosomal, 23S Recombination, Genetic Rhizobiaceae/genetics,physiology Sequence Homology, Nucleic Acid
Chemicals
DNA, Intergenic RNA, Ribosomal, 16S RNA, Ribosomal, 23S
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
van Berkum Peter
Soybean Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705, USA. pberkum@ba.ars.usda.gov
Terefework Zewdu
Paulin Lars
Suomalainen Sini
Lindström Kristina
Eardly Bertrand D
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Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.185.10.2988-2998.2003
Email
pberkum@ba.ars.usda.gov
Published
2003-05-00
Pages
2988-98
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC154066
Subset
IM
Corrections
CommentOn
PMID: 12730155
External Links
PubMed source DOI: 10.1128/JB.185.10.2988-2998.2003 PMC Full Text View journal details
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