ABSTRACT
We tested whether comparative sequence analysis of the mitochondrion-encoded cytochrome
c
oxidase subunit 2 gene (
COX2
) could be used to distinguish intraspecific variants of
Candida glabrata
. Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intraspecific variation. For this survey we used 11 clinical isolates of
C. glabrata
from three different geographical locations in Brazil, 10 isolates from one location in the United States, 1 American Type Culture Collection strain as an internal control, and the published sequence of strain CBS 138. The complete coding region of
COX2
was amplified from total cellular DNA, and both strands were sequenced twice for each strain. These sequences were aligned with published sequences from other fungi, and the numbers of substitutions and phylogenetic relationships were determined. Typing of these strains was done by using 17 substitutions, with 8 being nonsynonymous and 9 being synonymous. Also, cDNAs made from purified mitochondrial polyadenylated RNA were sequenced to confirm that our sequences correspond to the expressed copies and not nuclear pseudogenes and that a frameshift mutation exists in the 3′ end of the coding region (position 673) relative to the
Saccharomyces cerevisiae
sequence and the previously published
C. glabrata
sequence. We estimated the average evolutionary rate of
COX2
to be 11.4% sequence divergence/10
8
years and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of
COX2
sequences enables typing of
C. glabrata
strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphism that discriminates strains isolated in the United States and strains isolated in Brazil. This provides for the first time a means of typing of
Candida
strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.
Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA.
