Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications
for the Frequency of Horizontal Gene Transfer
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abstract
The current picture of bacterial evolution is based largely on studies of 16S
rRNA. However, this is just one gene. It is known that horizontal gene transfer
can occur between bacterial species, although the frequency and implications of
this are not fully understood. If horizontal transfer were frequent, there
would be no single evolutionary tree for bacteria because each gene would
follow a different tree. We carried out phylogenetic analyses of rRNA and tRNA
genes from Proteobacteria (a diverse group for which many complete genome
sequences are available) using RNA-specific phylogenetic methods that account
for the conservation of the secondary structure. We compared trees for 16S rRNA
and 23S rRNA with those derived from concatenated alignments of 29 tRNA genes
that are found in all the genomes studied. The tRNA genes are scattered
throughout the genomes, and would not follow the same evolutionary history if
horizontal transfer were frequent. Nevertheless, the tRNA tree is consistent
with the rRNA tree in most respects. Minor differences can almost all be
attributed to uncertainty or unreliability of the phylogenetic method. We
therefore conclude that tRNA genes give a coherent picture of the phylogeny of
the organisms, and that horizontal transfer of tRNAs is too rare to obscure the
signal of the organismal tree. Some tRNA genes are not present in all the
genomes. We discuss possible explanations for the observed patterns of presence
and absence of genes: these involve gene deletion, gene duplication, and
mutations in the tRNA anticodons.
