Biology Reference
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assorted 539,723 proteins encoded among 181 prokaryotic sequenced genomes to obtain matrices of
shared genes. The results revealed the existence of a network of shared genes and the genomes in
the network shared at least one gene family and thus are interconnected with each other forming a
complete network. They suggested that on the average 81±15% of the genes in each genome were
involved in LGT. Cyanobacteria possess 27±20% of genes acquired in their genomes through LGT.
The above account substantiates that the genomes of all organisms have evolved through LGT. If
that be so, how far is it feasible to trace the evolution of all organisms from a common ancestor? Is
it possible to construct a universal TOL? In addition to LGT, certain methodological problems that
lead to misleading phylogenies have been highlighted by Moreira and Philippe (2000). These are (i)
loss of phylogenetic signal by the accumulation of overlapping mutations, (ii) incongruity between
the real evolutionary process and the assumed models of sequence evolution and (iii) differences
of evolutionary rates among species or among positions within a sequence. According to Soria-
Carrasco and Castresana (2008) the inconsistencies or discrepancies that are generally encountered
in phylogenetic trees may also be due to phylogenetic artifacts or orthology assignment problems
instead of LGT events. They traced phylogenetic inconsistencies in the three domains of life and
the inconsistencies in phylogenetic trees of Proteobacteria and eukaryotes were more similar when
compared with the reference tree constructed on the basis of MLST approach.
All possible explanations have been put forward for building a universal TOL. Wolf
et al
. (2002)
suggested that LGT and differential gene loss are the major evolutionary phenomena in prokaryotes.
On the basis of complete gene sets it would be possible to construct a TOL. Phylogenetic analysis
of 220,240 proteins from 144 sequenced genomes resulted in the construction of a super tree of
prokaryotes that is consistent with 16S rDNA and other molecular sequence trees. Evidences
have been presented for the existence of LGT particularly among strains of
Prochlorococcus
and
Synechococcus
(Beiko
et al
., 2005). Clemente
et al
. (2006) created a data base (at address http://www.
jaist.ac.jp/~clemente/cgi-bin/phylo.pl.) for free public use meant for phylogenetic analysis based
on non-genomic data. This site consists of information on 13 organisms, 25 metabolic pathways and
>1000 enzymes, compounds and reactions. A sort of pseudo-alignment of metabolic pathways is
conducted that differs from a full alignment in the mapping being not necessarily one to one. The
pseudo-alignment from different organisms was done in order to assess their structural similarity.
The pseudo-alignment involved both graphic representation of each metabolic pathway as well as a
similarity measure between individual reactions, enzymes and compounds present in the pathway.
Using 61 of their 68 pathways, a phylogenetic analysis separated photosynthetic cyanobacteria
from eukaryotic photosynthetic organisms. However, within cyanobacteria, it was not possible
to distinguish the Chroococcales (
Synechocystis
,
Synechococcus
and
Thermosynechococcus elongatus
)
from the Prochlorales (
P
.
marinus
,
P
.
marinus
sub. sp.
pastoris
), the Nostocales (
Anabaena
) and the
Gloeobacterales (
Gloeobacter violaceus
). In case of other bacteria the phylogeny drawn from such
analysis was found to be consistent and reasonably close to the correct taxonomy based on sequence
data available with NCBI. Cottret
et al
. (2010) created a webserver known as Met Explore (freely
accessible for public use at http://metexplore.toulouse.inra.fr) having genome-scale reconstructed
metabolic networks to link metabolites identifi ed in untargeted metabolic experiments.
Beiko
et al
. (2005) are of the view that there might infact be no universal TOL and attempts to
construct such a universal TOL are futile in view of the rampant LGT events. In support of this
they presented a phylogenetic analysis of 220,240 proteins from 144 sequenced genomes from
which it was possible to construct a super tree that is remarkably congruent with 16S rDNA and
other molecular sequence trees. But the protein trees that are strongly incongruent with a super tree
node are discordant and provide evidence of LGT. This is more signifi cantly noted in thermophiles,
