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Intl. J. of Mol. Evol. and Biodivers. 2012, Vol. 2, No.1, 1-7
http://ijmeb.sophiapublisher.com
4
Table 1 The Euclidian distance of trinucleotide transition probability matrixes of bacterial genomes
L. lac
_MG
L. lac
_SK
L. lac
_I1
S. pyo
_M1
P. pen
_AT
S. aur
_US
A. met
_QY
L. lac
_MG
0
L. lac
_SK
0. 044
0
L. lac
_I1
0. 062
0. 073
0
S. pyo
_M1
0. 291
0. 295
0. 308
0
P. pen_AT
0. 321
0. 324
0. 324
0. 305
0
S. aur
_US
0. 392
0. 396
0. 390
0. 392
0. 334
0
A. met
_QY
0. 382
0. 388
0. 397
0. 320
0. 349
0. 372
0
Table 2 The joint histogram divergence of trinucleotide transition probability matrixes of bacterial genomes
L. lac
_MG
L. lac
_SK
L. lac
_I1
S. pyo
_M1
P. pen
_AT
S. aur
_US
A. met
_QY
L. lac
_MG
0
L. lac
_SK
35. 674
0
L. lac
_I1
87. 366
89. 496
0
S. pyo
_M1
1
020. 933
1
043. 886
1
202. 584
0
P. pen
_AT
1
090. 625
1
111. 164
1
193. 150
1
230. 305
0
S. aur
_US
1
291. 842
1
311. 779
1
324. 448
1
475. 062
1
062. 187
0
A. met
_QY
2
305. 814
2
344. 976
2
570. 574
1
586. 869
1
916. 826
1
768. 208
0
amplification effect on the diversity of genomes
comparing with other methods previous mentioned.
So, this new method we proposed performed higher
accurately and efficiently in estimating the evolutionary
distance of organisms for both closely related and
distantly related as our calculated results exhibited.
Moreover, another important conclusion that we
confirmed is the positive correlation between JHD and
their corresponding evolution distances exists for most
organisms, the closer relationship of organisms has,
and the smaller JHD is. However, there are exceptions
that JHD of close related organisms is larger than the
one of distant related organisms. Sometimes, which
may partly due to the universal occurrence of
horizontal gene transfer that caused high similarity of
genomic fragment of distant related organisms
(Gogarten and Townsend, 2005). Another reason is
probably the appearance of convergent evolution,
which could lead to the genome of distant related
organisms change analogously (Amoutzias et al., 2004).
Comparing with single-gene-based tree, this tree
based on image registration of oligonucleotide
transition probability matrices of microbial genomes
had clearer branched structure for taxa both above and
under the family level. Although this new method
might not be succeed to analyze the phylogenetic
relationship for some organisms and still be far away
from perfect, there is an extensive development
prospect to become a useful assistant tool or
enlightening mean in identification of unknown
organisms or phylogenetic inference (Tyagi et al.,
2010). It could determine the lineage of unknown
organisms by comparing with the definite organisms
using the image registration technology. Also, it might
be applicable on the genomes that have not been
annotated because there will be no need to obtain
homologous gene sequences and their multiple
alignments. Of course, this novel method for evolution
analysis we introduced needs further improvement and
development to become a really effective method for
species identification in the future.
3 Materials and Methods
3.1 Genomic sequences
We selected 100 bacterial genomes for this analysis.
Sequences data were obtained from NCBI website
(http://www.ncbi.nlm.nih.gov/genomes/). A list of full
binominal nomenclature with strain tags of these
organisms together with their NCBI accession
numbers and lineage codes is given in Supplement 1.
The “lineage code” given in the fourth column is
explained below.
As the taxons in NCBI only listed their names, we
have generated an explicit numbering for all taxon
ranking from phyla down to strains. For example,