Molecular Biology and Evolution, Vol 13, 451-461, Copyright © 1996 by Society for Molecular Biology and Evolution
V Cilia, B Lafay and R Christen
We have analyzed what phylogenetic signal can be derived by small subunit
rRNA comparison for bacteria of different but closely related genera
(enterobacteria) and for different species or strains within a single genus
(Escherichia or Salmonella), and finally how similar are the ribosomal
operons within a single organism (Escherichia coli). These sequences have
been analyzed by neighbor-joining, maximum likelihood, and parsimony. The
robustness of each topology was assessed by bootstrap. Sequences were
obtained for the seven rrn operons of E. coli strain PK3. These data
demonstrated differences located in three highly variable domains. Their
nature and localization suggest that since the divergence of E. coli and
Salmonella typhimurium, most point mutations that occurred within each gene
have been propagated among the gene family by conversions involving short
domains, and that homogenization by conversions may not have affected the
entire sequence of each gene. We show that the differences that exist
between the different operons are ignored when sequences are obtained
either after cloning of a single operon or directly from polymerase chain
reaction (PCR) products. Direct sequencing of PCR products produces a mean
sequence in which mutations present in the most variable domains become
hidden. Cloning a single operon results in a sequence that differs from
that of the other operons and of the mean sequence by several point
mutations. For identification of unknown bacteria at the species level or
below, a mean sequence or the sequence of a single nonidentified operon
should therefore be avoided. Taking into account the seven operons and
therefore mutations that accumulate in the most variable domains would
perhaps increase tree resolution. However, if gene conversions that
homogenize the rRNA multigene family are rare events, some nodes in
phylogenetic trees will reflect these recombination events and these trees
may therefore be gene trees rather than organismal trees.
ORIGINAL ARTICLE
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level
CNRS & Universite Paris, France.
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