GENOMES - Cyanobacteria - page 132

SS120. This clade is closer to 6 HL-strains rather than to P. marinus NATL1A and NATL2A clade.
On the other hand, sequence-based trees showed that P. marinus strains NATL1A and NATL2A are
closer to the HL-strains. They have further integrated the gene order data as well as concatenated
alignments and proposed that the situation can be resolved by proposing two alternative phylogenies.
In the fi rst, the clade with P. marinus strains MIT9211 and SS120 is closer to HL-strains where as in
the second the clade with P. marinus strains NATL1A and NATL2A is closer to HL-strains. Johnson
and Chisholm (2004) identifi ed overlapping genes that are adjacent and located on either of DNA
strands in the genomes of many microbes. These share one or more nucleotides in their coding
sequences. A comparison of such overlapping genes among 1352 orthologous genes in two closely
related strains of P . marinus (MIT9313 and MED4) revealed that there are 422 and 330 orthologues
that are part of an overlapping gene pair in P . marinus MIT9313 and MED4, respectively. Among
these orthologues, 69% and 83% in case of P . marinus MIT9313 and MED4, respectively have members
of the overlap pair as orthologues. They concluded that overlapping genes are not directly related
to either GC content or reduction in genome size but are more likely to be conserved. The order of
genes in chromosomes and nucleotide sequences appeared to be similar in 23 cyanobacteria whose
genomes have been compared by quantitative methods of estimation of gene order similarity. The
reconstructions of phylogenies based on the similarity of gene orders led to the suggestion that
genome rearrangements in marine picocyanobacteria are fi xed at a low rate while in other groups
the gene order can change very rapidly. The closest relatives of chloroplasts had been the strains of
Synechococcus from hotsprings and the existence of Synechococcus strains in different environments
(marine and freshwaters and hotsprings) is indicative of evolutionarily distant lines (Markov and
Zakharov, 2009).
Molecular synapomorphies are protein signature sequences that represent conserved portions or
indels that are specifi c to a group of taxa on the basis of which one can construct phylogenetic trees
and compare these with the whole genome-based or single gene-based (16S rRNA) phylogenetic trees.
Gupta (2009) compared phylogenetic trees constructed for 34 cyanobacterial sequenced genomes
based on concatenated sequences for 45 conserved proteins and also the 16S rRNA gene. Out of more
than 40 molecular signatures, 15 cyanobacteria-specifi c signature sequences have been identifi ed
that are helpful in delimiting several important taxonomic clades of cyanobacteria.
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