ISSN 1022-7954, Russian Journal of Genetics, 2009, Vol. 45, No. 8, pp. 906–916. © Pleiades Publishing, Inc., 2009.
Original Russian Text © A.V. Markov, I.A. Zakharov, 2009, published in Genetika, 2009, Vol. 45, No. 8, pp. 1036–1047.
Cyanobacteria is a large, diverse and ancient group
of prokaryotes playing an important role in global bio-
spheric cycles and in the development of life on the
Earth. Acquisition by cyanobacteria of the capability
for oxygenic photosynthesis, which presumably
occurred more than 2.5 billion years ago, has led to
oxygenation of the atmosphere and hydrosphere, thus
radically changing the habitats of living organisms and
creating prerequisites for the development of complex
forms of life. Cyanobacteria have also played a key part
in the development of an eukaryotic plant cell by pass-
ing to the endosymbiotic way of life and giving rise to
plastids. In the present-day biosphere, free-living and
symbiotic cyanobacteria continue playing a great role
through making a signiﬁcant contribution to the carbon
and nitrogen cycles [1–3].
A wide distribution, high ecological signiﬁcance,
and the evolutionary role of cyanobacteria have deter-
mined a great interest of researchers in this group of
prokaryotes and a large number of molecular genetic
studies. At present, genomes of over 20 species and
strains of cyanobacteria have been completely
sequenced and annotated [4–13].
The objective of this work is to reveal the main
trends of the evolution of gene orders in genomes of
cyanobacteria on the basis of comparative analysis of
the genomes with the use of quantitative estimation of
similarity of gene orders [14–19].
MATERIALS AND METHODS
Genomes of 23 cyanobacterium
strains available in the internet [http://www.
) were analyzed. The genomes of bacteria belong-
ing to taxa that are phylogenetically closest to cyanobacte-
(from the group Chlo-
(from the group
) were used as outgroups. For com-
parison, genomes of chloroplasts of the unicellular ﬂagel-
and the ﬂowering plant
were also used. Characteristics of
the genomes are presented in Table 1.
The order of arrangement in a chromosome of
732 orthologous protein-coding genes that are present
in all 23 examined strains of cyanobacteria was ana-
lyzed. In the genomes of the outgroups and chloro-
plasts, 387 of these genes were identiﬁed in
, 475 in
44 in the chloroplast of
and 51 in the chloroplast of
Orthologs were revealed using the GenePlot program
with subsequent removal of ambiguous and question-
able correspondences. Phylogenetic trees on the basis
of 16S rRNA were built up with the use of the Clustal
W program, and phylogenetic trees on the basis of gene
orders were built up with the use of the Phylip software
Evolution of Gene Orders in Genomes of Cyanobacteria
A. V. Markov
and I. A. Zakharov
Paleontological Institute, Russian Academy of Sciences, Moscow, 117997 Russia
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia
Received June 10, 2008
—Genomes of 23 strains of cyanobacteria were comparatively analyzed using quantitative methods
of estimation of gene order similarity. It has been found that reconstructions of phylogenesis of cyanobacteria
based on the comparison of the orders of genes in chromosomes and nucleotide sequences appear to be similar.
This conﬁrms the applicability of quantitative measures of similarity of gene orders for phylogenetic recon-
structions. In the evolution of marine unicellular planktonic cyanobacteria, genome rearrangements are ﬁxed
with a low rate (about 3% of gene order changes per 1% of 16S rRNA changes), whereas in other groups of
cyanobacteria the gene order can change several times more rapidly. The gene orders in genomes of cyanobac-
teria and chloroplasts preserve a considerable degree of similarity. The closest relatives of chloroplasts among
the analyzed cyanobacteria are likely to be strains from hot springs belonging to the genus
ative analysis of gene orders and nucleotide sequences strongly suggests that
strains from different
environments (sea, fresh waters, hot springs) are not related and belong to evolutionally distant lines.