DNA sequences of the gene tufA, encoding elongation factor Tu, were determined
from five cyanobacteria and 21 plastids. Three were full length (ca. 1230
bp) sequences from cloned DNA, and 23 were partial (ca. 740 bp) sequences
from PCR fragments. These sequences were aligned with sequences available
from the literature, creating a data set of 56 tufA sequences of eubacterial
or plastid origin. Phylogenetic analysis was performed on inferred amino
acid sequences with parsimony and neighbor joining techniques, and on first
and second position nucleotide sequences with maximum likelihood, and bootstrapping
was performed with each method. Trees determined by the three methods were
highly congruent with respect to well supported nodes. All examined plastids,
including those of green and red algae, chromophytes, and Cyanophora paradoxa,
cluster strongly with the cyanobacteria in all analyses. A cyanobacterial
origin of all plastids confirms phylogenetic analyses of 16S rRNA and atpB
sequences, but conflicts with those of rbcL and rbcS sequences. This discrepancy
may be attributable to an ancient gene transfer of the rubisco operon in
an ancestor of red algae and chromophytes. Maximum likelihood analysis also
provides some support for a monophyletic origin of all plastids, while neighbor
joining and parsimony analyses showed cyanobacteria and red, brown, and
green plastid lineages as an unresolved polytomy. These tufA analyses also
provide a broad perspective on eubacterial evolution, and in conjunction
with published rRNA trees, point to at least two major radiations within
eubacteria and their descendants: one of many eubacterial phyla, a second
of cyanobacteria, and possibly a third radiation early in plastid evolution.