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or not such genes are liable to be transferred through LGT and on the nature of gene product. When
gene order phylogenies are chosen, two important points are computed. These are breakpoint and
inversion distances. Breakpoint distances denote the number of gene adjacencies that are present
in one genome and absent in the other. So it reveals the dissimilarity of the gene order between
two genomes. An inversion distance is indicative of the minimum number of inversion events
that is required to convert one genome into another (Raubeson
et al
., 1992; Olmstead and Palmer,
1994; Blanchette
et al
., 1999; Belda
et al
., 2005; Wang
et al
., 2006). Kettler
et al
. (2007) identifi ed a
set of core genes common to 12 strains of
Prochlorococcus
and selected 100 such genes for drawing
phylogenetic relationships. The phylogenetic trees of all these genes are congruent with the 16S rRNA
and 16S-23S rRNA ITS phylogenies. Random regroupings of 100 such protein sequences (repeated
100 times) also yielded the same phylogeny and agreed with the topology derived from 16S rRNA
gene. However, the position of two LL-strains of
P. marinus
MIT9211 and SS120 differed. Likewise,
phylogenomics of 11 marine strains of
Synechococcus
based on concatenated alignments of 1,129
core proteins revealed phylogenetic trees consistent with 16S rRNA phylogeny. Two sub-groups
have been recognized within the sub-cluster 5.1. In one of the sub-groups strains of
Synechococcus
WH8102, CC0605, CC9902 and BL107 are clustered together while in the second sub-group other
strains of
Synechococcus
WH7803, WH7805, CC9311, RS9916, and RS9917 are grouped together. In
contrast, in the 16S rRNA tree the position of
Synechococcus
strains RS9916 and RS9917 remained
uncertain. Due to the fact that
Synechococcus
sp. strain RCC307 remained outside the sub-cluster
5.1, these workers preferred to create a new sub-cluster for this strain as 5.3 that has been consistent
with 16S rRNA phylogeny. They further concluded that (i) the ancestor for sub-cluster 5.3 diverged
even before the split between sub-cluster 5.1 and all other
Prochlorococcus
strains, and (ii) the rapid
diversifi cation process envisaged by Urbach
et al
. (1998) for marine picocyanobacteria seems to
hold good in explaining the dominance of
Prochlorococcus
and sub-cluster 5.1 of
Synechococcus
in
the marine ecosystem. Extending the criteria of average nucleotide identity (ANI) value of more
than 95% (in relation to RB of 70% of DNA:DNA hybridization) for defi ning a species put forward
by Konstantinidis and Tiedje (2005), these workers found that ANI appeared to be a better marker
to assign the strains to a particular clade. However, the average ANI values worked out for marine
picocyanobacteria centered around 87 to 91%, which is far below the level suggested by Konstantinidis
and Tiedje (2005) for proteobacteria. Dufresne
et al
. (2008) suggested that both rRNA gene identity and
ANI have fallen short to resolve the differences between the two
Prochlorococcus
and
Synechococcus
strains. Luo
et al
. (2008) subjected 12 genomes of
P. marinus
strains (MED4, MIT9515, MIT9312,
AS9601, MIT9301, MIT9215-HL strains; SS120, MIT9211, NATL2A, NATL1A, MIT9303, MIT9313-
LL) and one of
Synechococcus
strain (WH8102 as an outgroup) to BLASTCLUST analysis (a software
that is helpful in clustering sequences based upon at least 30% similarity over a minimum of their
50% lengths). This revealed the presence of 1131 orthologous genes shared by all the 13 genomes.
However, due to the existence of LGT and non-availability of any orhologous gene that is not liable
to LGT, these workers preferred to construct phylogenies based on the gene order. The breakpoint
and inversion distance-based phylogenies have been found to be consistent with the sequence-
based and gene content-based trees in showing all six HL-strains in a monophyletic cluster with
two clades (
P. marinus
MED4 and MIT9515 in the fi rst clade and the other four strains of
P. marinus
MIT9312, AS9601, MIT9301 and MIT9215 in the second clade). However, in case of LL-strains, the
inversion and breakpoint distance-based phylogenies showed the existence of two clusters (one for
P. marinus
NATL1A and NATL2A; and the other for
P. marinus
MIT9303 and MIT9313) consistent
with sequence-based trees. At the same time, the two gene order phylogenies also gave support to
the formation of a separate cluster for the two unresolved strains of
P. marinus
, i.e. MIT9211 and
