Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae?

Marianna Naum, Eric Wayne Brown, Roberta J. Mason-Gamer

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

The phylogenetic relationships of multiple enterobacterial species were reconstructed based on 16S rDNA gene sequences to evaluate the robustness of this housekeeping gene in the taxonomic placement of the enteric plant pathogens Erwinia, Brenneria, Pectobacterium, and Pantoea. Four data sets were compiled, two of which consisted of previously published data. The data sets were designed in order to evaluate how 16S rDNA gene phylogenies are affected by the use of different plant pathogen accessions and varying numbers of animal pathogen and outgroup sequences. DNA data matrices were analyzed using maximum likelihood (ML) algorithms, and character support was determined by ML bootstrap and Bayesian analyses. As additional animal pathogen sequences were added to the phylogenetic analyses, taxon placement changed. Further, the phylogenies varied in their placement of the plant pathogen species, and only the genus Pantoea was monophyletic in all four trees. Finally, bootstrap and Bayesian support values were low for most of the nodes, and all nonterminal branches collapsed in strict consensus trees. Inspection of 16S rDNA nucleotide alignments revealed several highly variable blocks punctuated by regions of conserved sequence. These data suggest that 16S rDNA, while effective for both species-level and family-level phylogenetic reconstruction, may underperform for genus-level phylogenetic analyses in the Enterobacteriaceae.

Original languageEnglish (US)
Pages (from-to)630-642
Number of pages13
JournalJournal of Molecular Evolution
Volume66
Issue number6
DOIs
StatePublished - Jun 1 2008

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Pathogens
Enterobacteriaceae
Ribosomal DNA
pathogen
Pantoea
phylogenetics
phylogeny
Phylogeny
plant pathogens
Genes
Pectobacterium
animal pathogens
Maximum likelihood
Erwinia
gene
Animals
Bayes Theorem
Brenneria
Conserved Sequence
Essential Genes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Naum, Marianna ; Brown, Eric Wayne ; Mason-Gamer, Roberta J. / Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae?. In: Journal of Molecular Evolution. 2008 ; Vol. 66, No. 6. pp. 630-642.
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Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae? / Naum, Marianna; Brown, Eric Wayne; Mason-Gamer, Roberta J.

In: Journal of Molecular Evolution, Vol. 66, No. 6, 01.06.2008, p. 630-642.

Research output: Contribution to journalArticle

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