Biological Sciences/Evolution
Genome Evolution in Cyanobacteria: the Stable Core and the Variable Shell
Tuo Shi*† and Paul G. Falkowski*‡§
*Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal
Sciences, and ‡Department of Geological Sciences, Rutgers, The State University of New Jersey,
New Brunswick, NJ 08901, USA
26 text pages, 7 figures and 3 tables
188 words in the abstract and total 36,149 characters in paper
Author contribution: T.S. and P.G.F. designed research; T.S. performed research; T.S. and P.G.F.
analyzed data; and T.S. and P.G.F. wrote the paper.
The authors declare no conflict of interest.
Abbreviations: LGT, lateral gene transfer; NJ, neighbor joining; ML, maximum likelihood; MP,
maximum parsimony; PCoA, principal coordinates analysis;
†Present
§To
address: University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064
whom correspondence should be addressed. Paul G. Falkowski, 71 Dudley Road, New
Brunswick, NJ 08901. E-mail: falko@marine.rutgers.edu, Telephone: (732)-932-6555 ext.370,
Fax: (732)-932-4083.
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Abstract
Cyanobacteria are the only known prokaryotes that perform oxygenic
photosynthesis, the evolution of which transformed the biology and geochemistry of
Earth. The rapid increase in published genomic sequences of cyanobacteria provides the
first opportunity to reconstruct events in the evolution of oxygenic photosynthesis on the
scale of entire genomes. Here we demonstrate the overall phylogenetic incongruence
among 682 orthologous protein families from 13 genomes of cyanobacteria. However,
principle coordinate analyses on the evolutionary relationships reveal a core set of 323
genes with similar evolutionary trajectories. The core set is extremely conservative in
protein variability, and is made largely of genes encoding the major components in
photosynthetic and ribosomal apparatus. Many of the key proteins are encoded by
genome-wide conserved small gene clusters which are indicative of protein-protein,
protein-prosthetic group and protein-lipid interactions. We propose that the
macromolecular interactions in complex protein structures and metabolic pathways retard
the tempo of evolution of the core genes, and hence exert a selection pressure that
restricts piecemeal lateral gene transfer of components of the core. Identification of the
core establishes a foundation for reconstructing robust organismal phylogeny in genome
space.
Keywords: cyanobacteria | gene family | lateral gene transfer | genome evolution |
oxygenic photosynthesis
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Introduction
Cyanobacteria are the only oxygenic photosynthetic prokaryotes. Approximately
2.4 billion years ago, the evolution of that energy transduction pathway transformed
Earth’s atmosphere and upper ocean, ultimately facilitating the development of complex
life forms that are dependent on aerobic metabolism (1-3). Molecular fossils of
cyanobacteria date back at least 3 Ga (4-8), and the clade has evolved into one of the
largest and most diverse groups of bacteria on this planet today (9). Cyanobacteria
contribute significantly to global primary production (10, 11), and diazotrophic taxa are
central to global nitrogen cycle (12-14). Arguably, this group, more than any other
prokaryotic phylum, has had a greater impact on the biogeochemistry and evolutionary
trajectory on Earth, yet its own evolutionary history is poorly understood.
The availability of complete sequences of genomes for clusters of related
organisms provides the first opportunity to reconstruct events of genomic evolution
through the analysis of entire functional classes (15). Currently, cyanobacteria represent
one of the densest clusters of fully sequenced genomes (Table 1). Comparisons of
genome sequences of closely related marine Prochlorococcus and Synechococcus species
have demonstrated an intimate link between genome divergence in specific strains and
their physiological adaptations to different oceanic niches (16, 17). This ecotypic
flexibility appears to be driven by myriad selective pressures that govern genome size,
GC content, gene gain and loss, and rate of evolution (18, 19). Moreover, phylogenetic
analyses of genes shared by all the five known phyla of photosynthetic bacteria, including
cyanobacteria (the only oxygenic group), purple bacteria (Proteobacteria), green sulfur
bacteria (Chlorobi), green filamentous bacteria (Chloroflexi), and the gram-positive
Genome Evolution in Cyanobacteria
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heliobacteria (Firmicutes), have provided important insights into the origin and evolution
of photosynthesis, an intensively debated subject in the past decades (20-31). This
information has been substantially extended by genome-wide comparative informatics
(32-34). One of the major implications of the latter work is a significant extent of lateral
gene transfer (LGT) among these photosynthetic bacteria. The observation that
cyanophages sometimes carry photosynthesis genes (35-38) provides one mechanism of
rapid LGT among these phyla. However, LGTs almost certainly do not occur with equal
probability for all genes. For example, informational genes (those involved in
transcription, translation, and related processes), which are thought to have more
macromolecular interactions than operational genes (those involved in housekeeping), are
seldom transferred (39, 40). The existence of a core of genes resistant to LGT has been
reported in recent studies using relatively intensive taxon sampling (41, 42), suggesting
that there exists a set of genes that remain closely associated, resistant to LGT, and with
an extremely slow evolutionary tempo. Identification of such core genes potentially
allows separatation of true phylogenetic signals from “noise”. It is, therefore, of
considerable interest to transcribe all coherent genome data into pertinent phylogenetic
information (43) and to identify which genes are more susceptible to lateral transfer.
Here we report on identification and reconstruction of the phylogeny of 682
orthologous protein families from 13 genomes of cyanobacteria. Our primary goals are
twofold: a) to examine the impact of LGT on the evolution of photosynthesis and the
radiation of cyanobacterial lineages; and b) to identify a core set of genes that are
resistant to LGT on which robust organismal phylogy can be reconstructed. Our results
reveal that >52% (359) of the orthologs are susceptible to LGT and hence are responsible
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for the inconsistant phylogenetic signal of this taxon in genome space. In contrast, the
remaining 323 othologs show broad phylogenetic agreement. This core set is comprised
of key photosynthetic genes as well as those coding for ribosomal translational apparatus.
This observation suggests that the macromolecular interactions in complex protein
structures (e.g., ribosomal proteins) and metabolic pathways (e.g., oxygenic
photosynthesis) are strongly resistant to piecemeal lateral gene transfer. Transfer was
ultimately accomplished by wholesale incorporation of cyanobacteria into eukaryotic
host cells, giving rise to primary photosynthetic endosymbionts which retained both
photosynthetic genes and genes encoding for its own ribosome (44-46).
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Results
Conserved protein families in genomes of cyanobacteria
Our pair-wise genome comparison revealed a total of 682 orthologous proteincoding genes that are common to all 13 genomes examined [supporting information (SI)
Table 2].
These genes constitute the core gene set and some of these define aspects of
the genotype that are uniquely cyanobacterial. This core set represents only 9.3% (in the
case of the largest genome Nostoc punctiforme) to 39.8% (in the case of the smallest
genome Prochlorococcus marinus MED4) of the total number of protein-coding genes
from each genome under study (see Table 1), but seems to account for all of the principal
functions in genome replication, expression, and repair, as well as the majority of the
reactions in several central metabolic pathways (SI Table 3). Our analysis is based on
identification of reciprocal best hits with a moderately customized BLAST e-value
threshold (10e−4) compared to what has been used by others (18, 19). This leads to an
estimate of the pool of orthologs similar to what has been identified from 10
cyanobacterial genomes (47), but nearly three times more than the number of
cyanobacterial signature genes bioinformatically characterized by Martin et al. (48), and
only 65% of the number of cyanobacterial clusters of orthologous groups (34). The
discrepancy mostly results, in the case of the former, from a filtering procedure to remove
homologs to chloroplasts and anoxygenic photosynthetic bacterial genomes, and in the
case of the latter, from a less stringent, unidirectional BLAST hit scheme employed. In
addition, some of the incomplete genomes used in this study are still undergoing
confirmation from the final assembly, and it is possible that equivalent genes have been
overlooked in some cases, resulting in an incomplete signature set. It is highly possible
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that both reciprocal and unidirectional, circular best BLAST hit schemes result in an
elimination of a large set of homolog families that are considered orthologs because of
the overly restrictive criterion (49). However, the reciprocal best hit criterion detects
more orthologs while producing the same qualitative results as the single best hit
approach (47). Indeed, even without the use of any particular threshold (i.e., the default
BLAST e-value threshold is 10), the set of orthologs identified via the reciprocal top
BLAST hit scheme probably underestimates the actual number of orthologs (19).
Phylogenetic incongruence among conserved protein families
Based on amino acid sequences, we built phylogenetic trees for each of the 682
orthologous protein families using both neighbor joining (NJ) and maximum likelihood
(ML) methods. To extrapolate major evolutionary trajectories, we analyzed and
compared the observed topologies from all 682 individual trees. Surprisingly, the
frequency distribution of observed topologies among the orthologous protein families
failed to reveal a predominant, unanimous topology that represents a large number of
orthologs (Fig. 1). In contrast, most of the orthologs (58% and 67% for NJ and ML,
respectively) select a particular topology by itself. As a result, the maximum number of
orthologs that share a particular topology is 15 and 13 for NJ and ML, respectively,
which accounts for only 1.9% to 2.1% of the orthologous datasets (Fig. 1). This result
clearly demonstrates the incongruence in phylogenetic information from individual
protein families, even though they are highly conserved among cyanobacterial taxa.
Phylogenomic reconcilement
To determine whether genes give completely incompatible phylogenetic
information or whether a common signal can be extracted from cyanobacterial
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phylogenies, we employed a series of phylogenomic approaches, including the consensus
of 682 individual trees, supertree reconstruction, as well as the reconstruction of
phylogeny based on a concatenated alignment of 192,423 sites from the 682 sequences.
These approaches greatly resolved the topological incongruence, leading to five
topologies as shown in Fig. 2. Specifically, the NJ and ML trees built with different
models using the concatenated sequences gave three topologies in total (T1 and T2 for
NJ; T2 and T3 for ML), one of which is in agreement with that of the small subunit
ribosomal RNA (SSU rRNA) tree repeatedly obtained with NJ, ML or maximum
parsimony (MP) methods. The consensus- and super-tree built on the 682 individual NJ
trees showed two other topologies (T4 and T5), whereas both the consensus- and supertree of ML trees revealed an identical topology to one of the concatenated ML trees.
These five topologies are remarkably similar in that Synechocystis sp. PCC 6803 (SYN,
see Table 1 for abbr. for other species) and five diazotrophic species form a monophyletic
clade ((SYN,CWA),(TER,(NPU,(ANA,AVA)))), and that Synechococcus WH8102 (SYW)
and three Prochlorococcus species form another monophyletic clade in three different
formats: (SYW,(PMT,(PMS,PMM))), ((SYW,PMT),(PMS,PMM)), and
(PMM,(PMS,(PMT,SYW))). The notable conflicts concern the species Synechococcus
elongates PCC 7942 (SCO) and the thermophilic Thermosynechococcus elongates BP-1
(TEL), which tend to cluster at the base of the two major conserved subgroups but form
aberrant topologies.
However, analyses of the fitness of a particular topology to the 682 sequence
alignments (SI Figs 6 and 7) indicated that almost all (97.5% to 99.6%) of the datasets
support topologies T1-T5 at the 95% confidence level (P=0.95). This result suggests that
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artificial paralogs or genes potentially obtained by LGT may thwart the establishment of
organismal relationships based on plural consensus of individual gene phylogenies.
The stable core and the variable shell in genome space
To characterize the evolutionary trajectories with regarding to remove artificial
paralogs, or genes potentially obtained by LGT, we calculated the tree distances among
all possible pairs of the orthologous sets. The pair-wise distances were then used to
conduct a principle coordinate analysis (PCoA). This resulted in a core set of 323 genes
that share similar evolutionary histories (i.e., co-evolving genes) as opposed to the other
359 that exhibit divergent phylogenies (i.e., independently evolving genes) (Fig. 3). It is
very striking that informational genes, especially those encoding ribosomal structural
components, are almost all grouped in the densest region, while the tail is formed largely
by operational genes. This observation is consistent with previous studies (39, 40) that
indicate phylogenetic information is highly conserved in informational genes.
Additionally, the core is comprised of key components constituting the scaffolds of the
photosynthetic apparatus, and proteins that participate in chlorophyll biosynthesis and the
Calvin cycle.
Using the sum of all possible pairwise genetic distance as a measure of the protein
variability (44), we compared the rates of evolution of genes in different functional
categories. A plot of frequency distribution of genes versus protein variability (Fig. 4)
reveals that ribosomal and photosynthetic genes are extremely conserved, whereas the
operational and other informational genes were strongly skewed toward higher protein
variability. This pattern of segregation is concordant with whether or not the genes are
located in the core, and whether or not they are organized in conserved gene clusters.
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This result suggests that the core gene set appears to have remained relatively stable
throughout the entire evolutionary history of cyanobacteria, while genes in the shell are
more likely to be acquired via LGT and are hence poorly conserved.
Finally, we chose the 323 core genes to reconstruct the organismal phylogeny.
The resulting tree, based on the concatenated core gene set, had the same topology as that
obtained from the concatenation of all the 682 genes and that for the consensus and
supertree of the trees obtained from all protein families (T3 in Fig. 2 and tree presented in
Fig. 5). It differed only slightly from other tested topologies that are not rejected by many
individual alignments (Fig. 2). Interestingly, the genomes from all the diazotrophic
cyanobacteria cluster as one main group; this clade appears to have acquired its nitrogen
fixation ability from a unicellular, thermophilic non-diazotrophic ancestor, probably
during the Archaean Eon. The early diazotrophs almost certainly were non-heterocystous
and eventually developed that differentiated cell type probably as a result of elevated
level of atmospheric O2 (50).
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Discussion
Our analyses reveal an overwhelming phylogenetic discordance among the set of
genes selected as likely orthologs (Fig. 1). Conflicting phylogenies can be a result of
either artifacts of phylogenetic reconstruction, LGT or unrecognized paralogy. In our
reciprocal best hit approach, we retained as orthologous gene families those containing
only one gene per species. Therefore, only orthologous replacement and hidden
paralogies (i.e., differential loss of the two copies in two lineages) can occur in selected
families. These two types of events are expected to be comparatively rare under strict
application of the reciprocal hit criterion (51). Thus, phylogenetic incongruence is
unlikely due to artifacts resulting from a biased selection of orthologous genes.
Furthermore, despite the overall disagreement in phylogenetic signal, most of the trees of
individual proteins gave unambiguously strong support for at least some particular subtopologies which are repeatedly obtained through consensus, supertree and even
concatenation analyses (Fig. 2). This finding obviates that phylogenetic incongruence is a
result of tree reconstruction artifacts or long branch attraction effects.
LGT is likely one of the most important driving forces that lead to the discrete
evolutionary histories of the conserved protein families. Indeed, LGT has played an
important role in the evolution of prokaryotic genomes (52-54). A hallmark of LGT is
that the transferred genes often exhibit phylogenic incongruity and/or aberrant organismal
distributions, which contrasts with the relationships inferred from both the SSU rRNA
tree and other most resolved phylogenies of vertically inherited individual protein-coding
genes. But how can this superficially random gene transfer event explain the conserved
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nature of many of the key genes that comprise the functional core across all
cyanobacterial taxa?
While phylogenomic approaches are capable of capturing the consensus and the
most frequently appeared bipartitions in individual phylogenies, leading to highly
conserved subgroups or clusters that silhouette the major trend in genome evolution, they
may not necessarily guarantee the paucity of a conflicting phylogenetic signal in genome
space. The plural support for the consensus / supertree / concatenation topologies
indicates that the five top topologies are not significantly different from each other at
P=0.95; or in other words, all the five topologies would be accepted by more than 90% of
the dataset using the same criterion because the data do not discriminate among the
topologies. Do the consensus / supertree / concatenation trees accurately reflect
organismal history? Or, on the contrary, do they blur the vertical inheritance signal by
incorporating potential LGT? There is a large margin of uncertainty. Part of the
uncertainty may be due to the strength of the SH test, especially when examining the
accuracy of similar topologies. Indeed, the SH test is based on the evaluation of only 15
candidate topologies out of a total of 13,749,310,575 possible unrooted tree topologies
for 13 species. Although the majority of the 13,749,310,575 possible topologies would
not be supported by any dataset, the selection of a limited number of trees may have
biased the analyses. But part of the uncertainty can also be attributed to the data, most
notably the poorly conserved proteins that are disturbed by LGT. This is even more
pronounced in the PCoA, which demonstrates clearly that about 53% of the orthologs are
subject to frequent lateral transfers that might have complicated/diluted the vertical
inheritance signal (Fig. 3).
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Our results reveal a core set of genes in cyanobacteria that share similar
evolutionary histories. The pattern of co-evolution of these genes is concomitant with
extraordinarily conserved protein primary structure (Figs. 4 and 5). This finding of
limited lateral transfer in highly conserved genes is consistent with the complexity
hypothesis; that is, genes coding for large complex systems that have more
macromolecular interactions are less subject to horizontal transfer than genes coding for
small assemblies of a few gene products (40). In addition to the ribosomal genes, a
significant number of photosynthetic genes are also clustered in the core, suggesting that
photosynthetic genes may be as constrained as the ribosomal genes through evolution. To
function effectively, the cyanobacterial photosynthetic apparatus needs an investment of
a huge number of proteins, pigments, cofactors, and trace elements. Moreover, genes
coding for the photosynthetic apparatus are scattered along the chromosome as small
clusters of two to four genes that are highly conserved among all cyanobacteria (55).
Although large-scale gene order has been shown to be relatively unstable in the
prokaryotic genomes (56-58), the conservation of a minimum number of essential
operons encoding proteins that function together in a pathway or structural complex
appears to prevent genes from being perturbed by LGT (55, 59). The complexity of
oxygenic photosynthetic machinery makes it difficult to transfer components piecemeal
to non-photosynsthetic prokaryotes. Indeed, operon splitting of the photosynthetic
apparatus requires many independent transfers of noncontiguous operons. Although
large-scale horizontal gene transfer among photosynthetic prokaryotes (32) may suggest a
complex non-linear process of evolution that results in a mosaic structure of
photosynthetic pathway (60), transfers of the key photosynthetic genes are very rare (36).
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Transfer of this key pathway was only achieved by wholesale incorporation of
cyanobacteria into eukaryotic host cells (44-46).
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Materials and Methods
Gene Family Selection
We performed all-against-all BLAST (61) comparisons of protein sequences for
all possible pairs of the 13 genomes of cyanobacteria (Table 1) using an e value of 10−4
as a lower limit cutoff, and reciprocal genome-specific best hits were identified. We
considered genes as being probable orthologs when they were included in an assembled
set comprising the 13 genomes in which each gene was each other’s best BLAST match.
A total number of 682 protein families consisting of one gene per genome were retrieved
and assigned to functional categories according to those defined for the cluster of
orthologous groups (COGs) (62). Because of the lack of a particular category for
photosynthetic genes, the latter were assigned to the “energy production and conversion”
COG category. Other genes which fell into more than one of the 19 COG categories have
been assigned to a supplemental category called “miscellaneous” (19).
Alignments and Tree Construction
Protein sequences were aligned with ClustalW (63) with manual corrections,
followed by selecting unambiguous parts of the alignments and concatenating sequences
excluding all gap sites with Gblocks program (64). The maximum likelihood (ML) trees
were computed for each family with the PHYML program (65) using the Jones, Taylor,
and Thornton (JTT) model of substitution (66) and the γ-based method for correcting the
rate heterogeneity among sites. For each family, the neighbor joining (NJ) trees were also
constructed using the distance matrix provided by TREE-PUZZLE program version 5.1
(67) under a γ-based model of substitution (alpha parameter estimated by PUZZLE, eight
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γ rate categories) and bootstrapped using SEQBOOT and CONSENSE from the PHYLIP
package version 3.6 (68).
Concatenation, consensus and supertree
To generate a set of reasonable candidate topologies that could be tested against
the alignments for individual gene, we used the consensus of the 682 trees from
individual protein families (two methods, yielding topologies T3 and T4 in Fig. 2), the
concatenation of all the proteins (192,423 amino acids) (seven methods, yielding
topologies T1 to T3), the supertree (two methods, yielding topologies T3 and T5), and the
SSU rRNA (three methods, yielding topology T1). In the case of the reconstruction of the
trees based on the SSU rRNA, we used the PHYLO_WIN (69) to perform the maximum
parsimony (MP), NJ with bootstrap, ML reconstruction using the γ-based method for
correcting the rate heterogeneity among sites. The consensus of the trees of the 682
protein alignments was obtained using the CONSENSE module of the PHYLIP package.
As there are no missing data, we also concatenated all the proteins and constructed the
tree either using the PROTML program in the MOLPHY package (70) or using the
quartet puzzling (QP) implemented with TREE-PUZZLE. Trees chosen for the supertree
computation were coded into a binary matrix using the coding scheme of Baum (71) and
Ragan (72). The matrices obtained were concatenated into a supermatrix. The supertree
was calculated on the supermatrix using program DNAPARS (default options) from the
PHYLIP package. Bootstrap values on the supermatrix were obtained using SEQBOOT
and CONSENSE.
Comparisons between Trees
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Trees were compared with Treedist program using the branch score distance of
Kuhner and Felsenstein (73). On the nn distance matrix obtained (n is the number of
trees), a principle coordinates analysis (PCoA) is computed using SAS software. PCoA,
a multivariate ordination method based on distance matrices, allowed us to embed our n
trees in a space of up to n-1 dimensions. By taking the most significant two first
dimensions and plotting the objects (the trees) along these, the major trends and
groupings in the data can be determined by visual inspection.
For each of the 682 alignments, a comparison of the likelihood of the best
topology with that of the candidate topologies (SI Fig. 6) was performed with the
Shimodaira-Hasegawa (SH) test (74) implemented in TREE-PUZZLE. This test
determines whether these potential organismal phylogenies are significantly rejected by
the alignment and thus whether LGT or some other anomalous process must be invoked.
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Acknowledgements
We thank William Martin and Colomban de Vargas for valuable comments and
stimulating discussions and Lin Jiang for help with the principle coordinates analysis.
This research is supported by NASA grants to P.G.F.. Sequence alignments and tree files
are available upon request.
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Genome Evolution in Cyanobacteria
Page 24
Tables
Table 1 General features of the genomes of the 13 cyanobacteria used in this study
Genome
Abbr.
Size
(mb)
(G+C)
%
Protein
coding
genes
Database
Reference
Anabaena (Nostoc) sp. PCC7120
Anabaena variabilis ATCC29413
Crocosphaera watsonii WH8501
Gloeobacter violaceus PCC7421
Nostoc punctiforme ATCC29133
Prochlorococcus marinus MED4
Prochlorococcus marinus MIT9313
Prochlorococcus marinus SS120
Synechococcus elongatus PCC7942
Synechococcus sp. WH8102
Synechocystis sp. PCC6803
(Thermo) Synechococcus elongatus BP-1
Trichodesmium erythraeum IMS101
ANA
AVA
CWA
GVI
NPU
PMM
PMT
PMS
SCO
SYW
SYN
TEL
TER
6.41
7.10
6.30
4.66
9.50
1.66
2.41
1.75
2.70
2.43
3.57
2.59
6.50
42.5
41.4
37.1
64.0
41.4
32.0
50.8
36.0
55.0
59.5
47.7
54.0
34.2
5,366
5,754
6,751
4,430
7,281
1,713
2,267
1,884
2,876
2,526
3,264
2,475
5,266
CyanoBase
JGI/DoE
JGI/DoE
CyanoBase
JGI/DoE
JGI/DoE
JGI/DoE
Roscoff
JGI/DoE
JGI/DoE
CyanoBase
CyanoBase
JGI/DoE
Kaneko et al., 01
Nakamura et al., 03
Meeks, 01
Rocap et al., 03
Rocap et al., 03
Dufresne et al., 03
Palenik et al., 03
Kaneko et al., 96
Nakamura et al., 02
Database website: CyanoBase (http://www.kazusa.or.jp/cyanobase/); JGI/DOE (http://www.jgi.doe.gov/);
Roscoff (http://www.sb-roscoff.fr/)
Genome Evolution in Cyanobacteria
Page 25
Figure legends
Fig.1. The distribution of tree topologies among 682 sets of orthologs. Both neighbor
joining (NJ, black bars) and maximum likelihood (ML, red bars) tree topologies gave
similar distribution pattern. There is no unanimous support for a single topology; rather
most of the orthologs (58% and 67% for NJ and ML trees, respectively) appeared as
singletons which associate with unique topologies.
Fig. 2. Representative backbone tree topologies. Phylogenetic trees were constructed
using both SSU rRNA gene and orthologous proteins through phylogenomic approaches
(see Materials and Methods for details). The phylogenetic tree construction methods are
highlighted with colored horizontal bars and text. The conserved monophyletic subgroups
in each topology (T1-T5) are shaded. The top panel shows the proportion of orthologs
giving a particular tree topology (NJ, black bar; ML, red bar). Also shown are the
examples of proteins corresponding to that topology. The bottom panel indicates number
of datasets accepting (left) or rejecting (right) a particular topology in a ShimodairaHasegawa (SH) (74) test of each of the backbone topologies along with other candidates
randomly obtained (SI Fig. 7). Note that the consensus topology (T3) is rejected by only
a few gene families. Species abbreviations as in Table 1.
Fig. 3. Principal coordinates analysis (PCoA) of trees compared with topological
distance. (A) Plot of the two first axes of the PCoA made from 628 ML trees. The other
54 genes are excluded as a result of axis demarcation. The same experiment with NJ trees
gave very similar results. The ellipse depicts 323 orthologs in the densest region (the
Genome Evolution in Cyanobacteria
Page 26
core) of the cloud that share a common phylogenetic signal, while trees present in the
marginal area (the shell) are much more likely to be perturbed by lateral transfers.
Photosynthetic genes are color coded based on their respective pathways. Also shown are
examples of conserved small clusters of ribosomal (red text) and photosynthetic (green
text) genes that are located in the core. (B) The PCoA plotted against the protein
variability. Photosynthetic genes are collectively designated as green dots. Note both the
ribosomal and key photosynthetic genes are extremely conservative in protein variability.
Fig. 4. Frequency distribution of the fraction of genes belonging to designated categories
within each 1.0 interval of protein variability. Protein variability was measured by taking
the total length of the corresponding tree obtained in the phylogenetic analysis as
measured by amino acid substitutions, divided by the number of sequences in the tree.
Fig. 5. The ML tree reconstructed based on the concatenation of the core 323 proteins.
The topology shown agrees with the consensus topology of the 682 orthologs (T3 of Fig.
2) and is supported by almost all individual datasets (Fig. 2 and SI Fig. 7).The divergence
of diazotrophic cyanobacteria is designated by the dashed line.
Genome Evolution in Cyanobacteria
Page 27
Figures
Number of topologies
500
NJ
ML
400
30
20
10
0
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15
Number of orthologs
Shi & Falkowski, Fig. 1
Genome Evolution in Cyanobacteria
Page 28
Shi & Falkowski, Fig. 2
Genome Evolution in Cyanobacteria
Page 29
1.0
A
Operational
Informational
Ribosomal
ATPase
Calvin cycle
Heme & Chlorophyll
PSI
PSII
Cyt. b6f
Dimension 2
0.5
NADH dehydrogenase
Ycf
0.0
rpl20/35; rpl27/21;
rpl3/4/23; rpl2/rps19;
rpl33/rps18; rpl12/10;
rpl22/rps3/rpl16;
rps17/rplN/24/5/rps8;
rpl6/18/rpsE/rpl15;
rps13/11/rpoA/rpl17;
rps12/7/fusA/tufA/rps10;
-0.5
psbEF; petBD; psaAB;
atpIH; atpAC; atpBE;
ndhFD; ndhAIGE
-1.0
-1.0
-0.5
0.0
0.5
1.0
Dimension 1
B
High
12
Operational
Informational
Ribosomal
10
Low
y
Protein variabilit
Photosynthetic
8
6
4
2
0
0.5
me
Di
0.0
2
ion
ns
1.0
-0.5
0.5
0.0
-1.0
-0.5
-1.0
sion 1
Dimen
Shi & Falkowski, Fig. 3
Genome Evolution in Cyanobacteria
Page 30
0.50
operational
informational
ribosomal
photosynthetic
Proportion
0.40
0.30
0.20
0.10
0.00
0.25
core
shell
Proportion
0.20
0.15
0.10
0.05
0.00
0.25
clustered
unclustered
Proportion
0.20
0.15
0.10
0.05
0.00
0
Low
2
4
6
8
10
Protein variability
12
High
Shi & Falkowski, Fig. 4
Genome Evolution in Cyanobacteria
Page 31
Shi & Falkowski, Fig. 5
Genome Evolution in Cyanobacteria
Table 2 legend
Page 1
Online Supporting Information
Table 2. Ortholog table including 682 conserved protein families from 13 genomes of
cyanobacteria. Column headings indicate ortholog ID, gene name, encoded protein, and
cyanobacterial species used in this study. Species abbreviation: ANA, Anabaena sp. PCC 7120;
AVA, Anabaena variabilis ATCC29413; CWA, Crocosphaera watsonii WH8501; GVI,
Gloeobacter violaceus PCC 7421; NPU, Nostoc punctiforme; PMM, Prochlorococcus marinus
MED4; PMS, Prochlorococcus marinus SS120; PMT, Prochlorococcus marinus MIT9313;
SCO, Synechococcus elongatus PCC7942; SYW, Synechococcus sp. WH8102; SYN,
Synechocystis sp. PCC 6803; TEL, Thermosynechococcus elongatus BP-1; TER, Trichodesmium
erythraeum IMS101. For species whose genomes were in draft form when this work was
undertaken, preliminary protein coding sequences were based on contig assemblies as of their
respective release dates: NPU, April 9, 2001; SCO, September 22, 2003; TER, December 16,
2003; AVA, January 19, 2005; CWA, January 30, 2004. The letters and numbers in each column
refer to the gene designators used by the individual genome projects, which are the likely
ortholog detected by the analysis reported here. In some cases, e.g., Nostoc, the name consists of
a contig followed by the gene number on that contig. In some cases the designator, e.g., sll0698,
indicates a relative direction of transcription too. Genes are tabulated for each functional
category in the physical order in which they occur in Synechococcus sp. WH8102. This allows
the identification of genome-wide conserved gene clusters (putative operons) containing two or
more signature genes by simply scanning the table. Signature genes included in these putative
operons are tabulated in italic. Informational (purple), ribosomal (pink) and photosynthetic genes
(green) are color shaded. Protein variability derived from the phylogenetic tree for each gene was
Online Supporting Information
Table 2 legend
Page 2
indicated. The binary number designates whether protein families were found in the core (1, also
in bold) or in the shell (0) of the genome as in Fig. 3.
Online Supporting Information
Table 2
Pag
ID
Prot.
Var.
Core
/
shell
ort343
ort539
ort537
ort186
ort190
ort210
ort364
ort087
ort017
ort392
ort341
ort145
ort149
ort452
ort453
ort369
ort648
ort347
ort002
ort484
ort046
ort394
ort647
ort156
ort585
ort596
ort267
ort344
ort308
ort224
ort026
ort331
ort170
ort437
ort174
ort232
ort177
ort673
ort460
ort565
ort630
4.8597
3.5725
7.7917
8.7381
5.9564
8.0168
3.5384
5.0449
3.9641
4.3684
3.4126
6.9095
5.2881
7.0501
8.0446
2.7995
6.5608
2.2050
4.0014
5.6054
6.6183
2.0643
2.9453
7.2478
2.5480
4.1919
8.0685
5.2289
2.1164
7.6150
4.3987
5.6049
3.5064
5.2913
8.5078
10.3689
4.3443
2.7635
4.4651
2.7893
2.7558
1
1
0
0
0
0
1
0
1
0
1
0
1
0
0
1
0
1
1
0
0
1
1
0
1
1
0
0
1
0
1
1
1
1
0
0
0
1
0
1
1
ANA
GVI
PMM
PMT
NPU
SCO
PMS
SYN
TEL
TER
SYW
AVA
CWA
Gene
Product
alr2010
all3652
all3651
all0443
alr4943
all1760
all1759
all1758
alr3887
alr2445
alr2447
alr2449
alr5067
alr5066
alr5065
all5062
alr5061
all5058
all5057
alr4755
all2847
all2846
all3519
alr3430
alr3428
asr3427
all4933
alr4932
alr3684
alr3681
all3680
all3679
all3678
alr3644
alr3444
all0932
all3013
all1132
alr3638
alr3993
alr4851
glr3232
glr2113
glr2114
gll1546
gll1464
gll1336
glr0251
glr1672
gll1051
gll4194
glr4267
glr4268
glr3498
glr2317
glr2316
glr0530
glr3298
glr1285
glr1286
glr0970
gll1629
glr2615
gll1807
gll0286
gll2784
gsl2785
glr2559
glr1609
glr4196
glr4195
glr1017
glr1018
glr1019
gll1774
gll0066
gll0401
glr4006
gll1855
gll1033
glr1042
gll1836
0001
0003
0004
0006
0007
0009
0010
0011
0012
0016
0017
0019
0020
0021
0022
0023
0024
0026
0027
0028
0036
0037
1664
1663
1662
1661
1659
1658
1657
1655
1654
1653
1652
1648
1647
1651
1650
1649
1645
1643
1639
0001
0003
0004
0006
0007
0010
0011
0012
0013
0021
0022
0024
0025
0026
0027
0028
0029
0031
0032
0033
0044
0045
0052
0054
0055
0056
0058
0059
0061
0063
0064
0065
0066
0073
0074
0068
0069
0071
0079
0081
0083
424.5
430.35
430.36
483.77
485.23
506.137
506.138
506.142
432.30
506.170
506.172
506.174
418.36
418.34
418.33
418.18
418.32
418.21
418.22
505.73
472.81
472.82
505.205
498.153
498.151
498.150
505.147
505.44
448.70
448.68
448.8
448.9
448.10
482.108
505.39
501.71
439.16
418.3
504.24
509.108
427.41
136.2572
136.2574
136.2575
136.2839
136.2838
129.527
129.528
129.529
129.531
135.1882
135.1884
135.1886
136.2277
135.2117
135.2116
135.1726
129.567
129.576
129.577
132.998
136.2428
136.2429
136.2864
128.510
128.507
128.506
134.1557
126.225
129.548
129.546
135.2061
135.2062
135.2063
134.1469
136.2783
134.1586
134.1395
136.2222
130.690
130.693
136.2714
0001
0003
0004
0006
0007
0009
0010
0011
0012
0016
0017
0019
0020
0021
0022
0023
0024
0026
0027
0028
0037
0038
1824
1823
1822
1821
1819
1818
1817
1815
1814
1813
1812
1808
1807
1811
1810
1809
1805
1803
1801
slr0965
sll1056
sll0757
sll0837
sll1348
sll0271
slr2102
slr2031
slr1133
sll0057
sll0897
sll0898
slr1847
slr1424
slr1423
sll1342
slr1787
slr0434
slr0435
sll0660
slr1538
slr0213
slr0633
slr0171
sll0767
ssl1426
sll1377
sll1360
sll0535
sll0533
slr0549
slr0550
slr0551
slr0657
sll0544
slr1278
slr2032
sll0459
sll1165
sll1282
sll0616
tll2349
tlr1683
tlr1684
tll2091
tlr0587
tll0787
tlr0928
tlr2236
tll0366
tlr1314
tll0790
tll0987
tlr0723
tll0370
tll0371
tll1466
tll2366
tlr1294
tlr1295
tll2045
tlr0767
tll2418
tll0065
tll2406
tll2158
tsl2159
tlr1854
tlr1132
tlr0510
tlr0508
tlr0069
tlr1219
tlr1220
tlr1833
tlr1573
tlr1616
tlr1249
tlr2033
tlr2240
tlr0067
tll1851
97.8656
122.6536
119.4070
118.3826
120.5163
118.3710
118.3711
118.3712
118.3713
111.1619
111.1622
111.1625
120.4678
120.4677
120.4676
120.4961
120.4675
112.1685
112.1688
95.8488
114.2291
114.2292
122.6785
119.4203
119.4201
119.4200
121.5205
116.2672
118.3957
118.3955
118.3578
118.3579
118.3580
96.8564
107.800
121.5631
122.7130
122.7522
119.4444
103.289
122.6969
0001
0003
0004
0006
0007
0010
0011
0012
0013
0023
0024
0026
0027
0028
0029
0030
0031
0033
0034
0035
0046
0047
0054
0056
0057
0058
0060
0061
0063
0065
0066
0067
0068
0070
0073
0075
0076
0077
0078
0082
0086
232.3907
232.2534
232.2535
232.1788
232.1191
232.4168
232.4169
232.4170
232.786
232.4265
232.4267
232.4269
232.1283
232.1282
232.1281
232.1279
232.1278
232.1276
232.1275
232.893
232.4920
232.4921
232.2129
232.2353
232.2351
232.2350
232.1179
232.1178
232.2502
232.2504
232.2505
232.2506
232.2507
232.2540
232.2371
232.4394
232.4766
232.3538
232.2097
232.686
232.1095
358.4593
358.4475
358.4479
361.5946
362.6447
359.4742
235.1403
241.1494
241.1495
278.2040
231.1351
361.5601
295.2370
361.5931
361.5930
201.980
211.1112
359.4728
359.4729
332.3322
362.6013
361.5637
362.6674
329.3240
361.5828
361.5827
358.4612
321.3017
319.2952
122.331
336.3450
336.3451
336.3452
284.2172
317.2914
267.1864
361.5613
361.5490
341.3608
346.3807
270.1905
dnaN
purL
purF
DNA polymerase III beta subunit
phosphoribosylformylglycinamidine synthetase II
Glutamine amidotransferase class-II:Phosphoribosyl
conserved hypothetical protein
conserved hypothetical protein
NusB family protein
signal recognition particle docking protein FtsY
conserved hypothetical protein
Fumarate lyase:Delta crystallin
putative heat shock protein GrpE
DnaJ protein
conserved hypothetical protein
conserved hypothetical protein
UDP-N-acetylenolpyruvoylglucosamine reductase
Probable UDP-N-acetylmuramate-alanine ligase
glyceraldehyde 3-phosphate dehydrogenase (NADP
putative thiamine monophosphate kinase
Translation elongation factor EF-P
biotin carboxyl carrier protein (BCCP) subunit of ac
putative pyridoxal phosphate biosynthetic protein Pdx
cobalamin biosynthesis protein D
GMP synthase (glutamine-hydrolysing)
thiamin biosynthesis protein
conserved hypothetical protein
50S ribosomal protein L20
50S ribosomal protein L35
putative glycosyltransferase
DNA polymerase, gamma and tau subunits
Putative ATP-dependent protease ATP-binding su
Possible FKBP-type peptidyl-prolyl cis-trans isomera
aspartate-semialdehyde dehydrogenase
dihydrodipicolinate synthase
conserved hypothetical protein
aspartate kinase
conserved hypothetical protein
possible MesJ homolog
conserved hypothetical protein
excinuclease ABC subunit B
putative DNA mismatch repair protein
Putative 6,7-dimethyl-8-ribityllumazine synthase o
preprotein translocase SecA subunit
Online Supporting Information
ftsY
argH
grpE
dnaJ
murB
murC
gap2
thiL
efp
accB
pdxA
cbiD
guaA
thiG
ycf37
rpl20
rpl35
dnaX
clpX
asd
dapA
lysC
uvrB
mutS
ribH
secA
Table 2
Pag
ort327
ort189
ort420
ort445
ort397
ort263
ort009
ort641
ort438
ort638
ort627
ort296
ort645
3.4146
5.5755
2.6576
6.7596
2.1798
8.6248
7.0173
2.6652
4.3220
3.5393
4.3404
4.0367
1.2772
1
1
1
0
1
0
0
1
0
1
0
1
1
all4037
all1076
all4623
alr5266
all5265
alr0517
alr1414
alr0088
all4071
alr5070
all2894
all2102
all0982
glr2514
glr4252
gll1756
gll3248
gll2506
gll0502
glr3183
glr2942
gll3356
gll1494
gll3119
glr2540
glr1118
1638
1637
1636
1635
1634
1627
1625
1623
1618
1616
1615
1613
1611
0117
0118
0119
0120
0121
0136
0138
0141
0147
0155
0156
0158
0160
479.50
448.6
483.54
483.83
483.40
454.52
476.44
444.42
507.275
418.38
431.9
389.22
504.76
125.197
136.2611
136.2498
129.624
129.537
136.2624
127.357
136.2723
125.172
135.2092
132.1024
135.1997
134.1422
1800
1799
1798
1797
1796
1788
1786
1784
1779
1776
1775
1773
1771
slr1348
sll1961
slr0974
sll0817
sll2005
slr1448
sll1234
slr0925
slr1550
slr1639
sll0613
sll0100
slr0118
tlr0851
tll2117
tlr1620
tlr0648
tll0647
tll1428
tll2390
tlr1490
tll0212
tll1927
tll2253
tll0013
tlr0334
99.8760
105.623
114.2168
120.4905
120.4740
121.6195
122.7559
101.106
115.2623
115.2649
112.1715
119.4412
105.559
0090
0091
0093
0094
0095
0117
0119
0121
0127
0134
0135
0137
0140
232.652
232.2627
232.1009
232.1471
232.1470
232.1845
232.2846
232.5313
232.2062
232.1286
232.4875
232.4927
232.4245
354.4128
286.2198
362.6249
361.5471
362.6726
52.32
360.5181
351.3997
362.6074
361.5795
289.2256
361.5413
361.5939
ort652
ort349
ort005
ort518
ort380
ort566
ort091
ort093
ort411
ort294
ort234
ort526
ort528
ort524
ort523
ort288
ort626
ort468
ort474
ort124
ort218
ort216
ort298
ort358
ort335
ort135
ort351
ort406
ort139
ort211
3.4278
3.4950
3.9182
0.3821
4.1998
6.0249
11.8245
7.1695
3.8460
3.9272
10.7885
3.3219
1.9807
2.1270
3.1238
5.6687
4.4346
1.9352
4.2351
4.5468
6.1874
10.6923
3.0127
8.3583
6.2350
5.5160
2.9287
2.6944
7.0841
6.2244
1
1
1
1
1
0
0
0
1
1
0
1
0
1
1
0
1
1
1
1
1
0
1
0
1
0
1
1
0
0
alr3344
alr3343
asr3342
asr3463
alr3464
alr2812
alr2709
alr3454
all1897
all4495
all3989
asr3848
asr3847
asr3846
asr3845
alr3844
alr3843
all3842
all3840
alr2298
alr0180
alr0181
all0278
asr2953
alr3012
all0513
all4391
all4390
all5088
all5089
glr2297
gll4014
glr2311
gsl3287
gll2215
gll1505
gll2564
gll0917
gll0410
glr2394
gll1453
gsr0859
gsr0858
gsr0857
gsr0856
glr0855
glr0854
glr0748
glr0750
glr4164
glr4114
glr4115
glr0870
glr2647
glr1861
glr2108
glr4188
gll0769
glr0532
glr0388
1610
1609
1608
1607
1606
1605
1598
1597
1594
0304
0303
0300
0299
0298
0297
0296
0295
0294
0292
0291
0290
0289
0288
0287
0284
0283
0282
0281
0279
0278
1957
1956
1955
1954
1953
1951
1942
1938
1685
1917
1910
1899
1898
1897
1896
1895
1894
1893
1891
1890
1889
1888
1887
1886
1884
1883
1881
1880
1872
1871
373.12
373.11
373.9
507.20
507.21
443.69
493.69
504.121
400.25
463.56
509.252
493.54
493.53
493.52
493.51
493.50
493.49
493.109
493.111
481.60
495.86
495.87
480.38
482.47
439.69
397.10
493.129
493.131
475.25
475.24
136.2842
136.2841
136.2840
136.2232
136.2233
131.788
132.1078
129.614
135.1786
130.671
134.1487
134.1370
134.1369
134.1368
134.1367
134.1366
134.1365
134.1603
134.1605
136.2771
136.2751
136.2752
131.792
131.923
136.2493
135.1719
136.2459
136.2460
128.515
128.513
1770
1769
1768
1767
1766
1764
1756
1753
1750
0335
0334
0331
0330
0329
0328
0327
0326
0325
0323
0322
0321
0320
0319
0318
0316
0315
0314
0313
0311
0310
sll1070
sll1069
ssl2084
ssl0563
sll0220
slr0808
slr1438
slr1342
sll1184
sll1143
sll1253
smr0008
smr0007
smr0006
ssr3451
slr2034
slr2033
slr1279
slr1281
sll0154
sll1001
sll1002
slr1777
slr1093
slr1666
sll1289
slr1051
slr0500
slr0402
slr1334
tll1870
tll1871
tsl1872
tsl1013
tll1237
tlr1065
tll1673
tll2430
tll0365
tlr2459
tll0519
tsr1544
tsr1543
tsr1542
tsr1541
tll1695
tll1696
tlr1429
tlr1430
tlr1951
tll0328
tll2407
tll1413
tll0178
tlr0710
tlr1788
tll1693
tll0133
tll1797
tlr1520
122.6452
122.6451
122.6450
122.7684
122.7687
122.7168
120.4906
111.1637
116.2796
104.450
103.378
106.653
106.652
106.651
106.650
106.649
106.648
106.714
106.716
109.1102
109.1205
109.1206
102.249
118.3672
93.8356
122.7432
87.8161
87.8165
122.7783
119.4338
0141
0142
0143
0144
0145
0149
0160
0162
0171
0181
0188
0201
0202
0203
0204
0205
0206
0207
0209
0210
0211
0212
0213
0216
0220
0221
0225
0226
0234
0235
232.2543
232.2544
232.2545
232.2386
232.2387
232.4959
232.3146
232.2378
232.2660
232.2265
232.690
232.5532
232.829
232.830
232.831
232.832
232.833
232.834
232.836
232.4018
232.1612
232.1613
232.2001
232.4816
232.4767
232.1841
232.2190
232.2191
232.1328
232.1327
361.5431
362.6015
362.6014
361.5974
362.6625
301.2515
342.3654
361.5829
359.4859
207.1070
358.4650
86.164
86.163
86.162
86.161
86.160
86.159
174.729
174.731
296.2411
343.3660
343.3661
238.1440
274.1977
216.1168
361.5903
186.837
282.2133
349.3910
322.3044
Online Supporting Information
cysE
infC
miaA
gyrB
ahcY
ssb
lysS
smpB
ruvB
thiC
cbbT,
tktA
fabF
acpP
psaC
glmS
rimM
ho1
psbJ
psbL
psbF
psbE
ycf48
rub
ndhC
ndhJ
chlD
folK
degT
fabI
hisB
serine acetyltransferase
conserved hypothetical protein
translation initiation factor IF-3
tRNA delta-2-isopentenylpyrophosphate (IPP) transfe
DNA gyrase subunit B
Putative fructokinase
putative adenosylhomocysteinase
single-stranded DNA-binding protein
lysyl-tRNA synthetase
tmRNA binding protein SmpB
Holliday junction DNA helicase RuvB
Zinc metallopeptidase M20/M25/M40 family
thiamin biosynthesis protein
transketolase
3-oxoacyl-[acyl-carrier-protein] synthase II
acyl carrier protein (ACP)
photosystem I iron-sulfur center subunit VII (PsaC
Glutamine--fructose-6-phosphate transaminase (is
possible 16S rRNA processing protein RimM
conserved hypothetical protein
conserved hypothetical protein
Heme oxygenase
UvrD/REP helicase
possible polyA polymerase
putative photosystem II reaction center J protein
photosystem II reaction center L protein (psII 5 Kd pr
Cytochrome b559 beta chain
cytochrome b559 alpha chain
similar to plant photosystem II stability/assembly fact
probable rubredoxin
NADH dehydrogenase I chain 3 (or A)
NADH dehydrogenase I chain J
conserved hypothetical protein
possible ABC transporter, ATP-binding componen
possible ABC transporter
Protoporphyrin IX Magnesium chelatase subunit C
possible 2-amino-4-hydroxy-6-hydroxymethyldihydro
putative pleiotropic regulatory protein
conserved hypothetical protein
enoyl-[acyl-carrier-protein] reductase
imidazoleglycerol-phosphate dehydratase
conserved hypothetical protein
Phosphoglucomutase/phosphomannomutase family p
Table 2
ort547
ort247
ort527
ort644
ort320
ort142
ort243
ort439
ort290
ort143
ort388
ort063
ort427
ort144
ort529
ort525
ort531
ort146
ort147
ort148
ort475
ort666
ort414
ort372
ort545
ort336
ort530
ort326
ort022
ort150
ort054
ort053
ort055
ort201
ort295
ort003
ort151
ort253
ort533
ort383
ort152
ort679
ort048
ort363
Pag
6.8194
3.9718
2.5918
3.8372
8.6386
2.6218
10.1699
3.4945
5.6424
7.2182
2.8950
5.8566
9.6463
10.3707
4.9395
3.1472
6.4828
5.8805
8.2031
5.1328
2.6719
8.6804
4.1862
6.4063
4.2890
7.3614
6.1353
13.9143
5.1566
6.6164
1.9188
3.4352
9.8770
4.1417
4.9136
2.7860
6.7278
8.3556
3.5702
1.9370
5.6983
7.5593
6.8278
7.0142
0
1
0
1
0
0
0
1
0
0
1
0
0
0
1
1
0
0
0
0
1
0
1
1
0
0
0
0
0
0
1
1
0
1
0
1
0
0
1
1
0
0
0
0
alr5099
all5094
asl0885
alr1885
alr0379
asl3981
all3113
all0985
alr3085
all0185
alr4806
alr4808
all1416
alr1278
asr0847
asl0846
all0844
asl4395
alr4394
alr4393
alr4392
alr0570
alr1073
asl3192
all1681
all3111
all3854
all5138
all0797
all2705
alr2492
alr2493
alr2494
all4087
asl0940
alr0939
alr4005
alr1128
alr3395
all2319
all1162
alr3123
alr3122
all0154
gll4276
glr1860
gsr2807
glr0802
gll3727
gll0064
gll3761
glr3299
gll1734
gll1471
glr4369
glr2441
glr3418
gll3632
gsl3001
gsr3002
gll0538
gsr0107
gll2308
gll2309
gll3285
glr1718
gll3651
gsl3282
gll2875
glr1548
glr3691
glr1084
glr3393
glr4150
glr1370
glr1371
glr1372
gll0929
gsr2010
gll2012
glr2712
glr3322
glr0043
gll0256
gll3593
glr2021
glr1719
gll3581
Online Supporting Information
0275
0273
0272
0271
0270
0268
0267
0264
0262
0261
0258
0257
0255
0254
0252
0251
0250
0249
0248
0247
0246
0242
0238
0235
0233
0229
0228
0227
0224
0075
0073
0072
0071
0067
0061
0060
0059
0057
1465
1463
1461
1460
1459
1458
1868
1865
1863
1862
1861
1859
1858
1854
1852
1851
1847
1845
1843
1841
1838
1837
1835
1834
1833
1832
1831
1826
1817
1815
1807
1802
1800
1799
1795
1608
1606
1605
1604
1596
1589
1588
1587
1584
1484
1481
1478
1477
1476
1475
475.89
475.17
509.247
509.246
509.116
507.159
489.110
490.102
397.16
492.138
356.2
356.3
459.4
492.17
501.138
501.108
501.110
493.128
493.20
493.19
493.18
509.177
406.27
387.11
378.7
489.112
502.159
458.5
466.46
388.13
502.169
502.171
502.172
494.47
501.60
501.176
504.190
479.56
397.35
475.84
501.196
469.13
469.12
502.44
136.2543
136.2563
136.2807
136.2806
136.2284
136.2285
136.2804
136.2491
135.1953
135.1872
136.2375
136.2377
129.560
135.1701
136.2405
136.2679
136.2681
136.2682
136.2629
136.2628
136.2627
130.771
125.157
131.821
127.391
136.2717
136.2719
136.2720
136.2674
126.256
135.1721
135.1722
135.1723
133.1220
135.1861
133.1255
133.1225
135.1948
136.2360
136.2358
135.2064
136.2357
136.2356
136.2355
0307
0305
0304
0303
0302
0300
0299
0296
0294
0293
0290
0289
0287
0286
0284
0283
0281
0280
0279
0278
0277
0272
0268
0265
0262
0258
0257
0256
0253
0088
0086
0085
0084
0080
0075
0074
0073
0071
1619
1616
1614
1613
1612
1611
slr0185
slr0338
sml0005
slr0713
slr0636
sml0011
sll1284
slr0348
sll2014
slr0488
sll1931
slr0427
sll1444
sll0350
smr0009
ssl2598
slr0922
sll1340
sll0832
sll1424
sll1423
sll1980
sll1362
slr0033
slr1476
sll0250
sll0427
slr1165
sll1747
sll0185
slr0074
slr0075
slr0076
slr1234
ssl0353
sll0053
slr1677
sll1120
sll0421
ssl0707
slr0711
slr2087
sll0621
slr1267
tlr1828
tll1731
tsl0176
tll0080
tll1337
tsr1779
tlr2038
tlr1041
tlr1697
tll2350
tlr2127
tlr2129
tlr1234
tlr1075
tsr1387
tsl1386
tll1384
tsl2214
tlr0651
tll1784
tll1650
tlr0355
tlr2330
tsl1524
tll1558
tll2467
tll0444
tll1044
tll0463
tll2067
tll0490
tlr1904
tlr1905
tlr0997
tlr1577
tlr1808
tll1550
tlr1925
tll1829
tll0591
tll0218
tll0683
tlr0052
tlr0440
105.603
110.1335
120.4838
105.566
105.600
120.4861
122.6578
121.5850
122.6657
122.7476
122.6602
122.6605
108.1038
121.5706
104.494
104.396
104.398
104.402
87.8177
87.8176
87.8174
122.6363
86.8139
122.7025
117.3410
122.6581
120.4767
122.7556
104.495
122.7320
117.3395
117.3396
117.3397
107.845
121.5436
121.5934
121.5738
122.6323
120.4569
121.6103
121.5909
118.3934
118.3933
122.6816
0238
0240
0243
0244
0245
0247
0248
0252
0254
0255
0259
0261
0263
0265
0268
0269
0271
0272
0273
0274
0275
0280
0289
0292
0296
0301
0303
0304
0308
0313
0319
0320
0321
0328
0335
0336
0337
0341
0405
0462
0463
0471
0472
0475
232.1318
232.1323
232.3352
232.2648
232.1757
232.701
232.2703
232.1875
232.3711
232.1616
232.1047
232.1049
232.2848
232.1923
232.3317
232.3316
232.3314
232.2186
232.2187
232.2188
232.2189
232.4228
232.2666
232.2776
232.5037
232.2701
232.820
232.1341
232.4469
232.3142
232.4311
232.4312
232.4313
232.4692
232.4400
232.4399
232.682
232.3545
232.2313
232.4038
232.3283
232.2714
232.2713
232.5371
357.4370
289.2251
361.5328
362.6159
256.1697
321.2998
304.2597
360.4968
359.4836
345.3723
360.5077
362.6743
216.1169
362.6423
319.2958
305.2618
214.1136
332.3321
186.836
186.835
186.834
361.5842
360.4887
253.1647
362.6596
192.895
359.4858
259.1746
280.2085
275.2006
264.1818
264.1819
362.6578
361.5735
333.3352
328.3194
362.6426
282.2136
355.4168
361.5924
321.3011
355.4178
355.4177
360.5218
pyrE
psbK
tgt
cobS
lytB
glyA
leuD
psbN
psbH
pth
ntcA
txlA
ileS
gatC
pyrB
dfp
psbO
cysD
aroC
accC
purB
glnB
ycf44
ccdA
ftsW
Orotate phosphoribosyltransferase
probable oxidoreductase
photosystem II 4 Kda protein psbK precursor
tRNA-guanine transglycosylase
Cobalamin-5-phosphate synthase CobS
conserved hypothetical protein
probable esterase
LytB protein homolog
sugar fermentation stimulation protein
conserved hypothetical protein
serine hydroxymethyltransferase (SHMT)
CinA-like protein
3-isopropylmalate dehydratase small subunit
conserved hypothetical protein
Photosystem II reaction centre N protein (psbN)
Photosystem II 10 kDa phosphoprotein (PsbH)
putative peptidyl-tRNA hydrolase (PTH)
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
Global nitrogen regulatory protein, CRP family of
thioredoxin-like protein TxlA
isoleucyl-tRNA synthetase
glutamyl-tRNA (Gln) amidotransferase subunit C
aspartate carbamoyltransferase
putative p-pantothenate cysteine ligase…
photosystem II manganese-stabilizing polypeptide
ATP-sulfurylase
Chorismate synthase
conserved hypothetical protein
ABC transporter, membrane component
ABC transporter, ATP-binding component
ABC transporter, membrane component
HIT (Histidine triad) family protein
YGGT family, conserved hypothetical integral memb
acetyl-CoA carboxylase, biotin carboxylase subuni
conserved hypothetical protein
putative chromosome segregation protein, SMC ATPa
Fumarate lyase:Adenylosuccinate lyase
nitrogen regulatory protein P-II
conserved hypothetical protein
putative c-type cytochrome biogenesis protein Ccs1
putative c-type cytochrome biogenesis protein CcdA
Cell division protein FtsW
Table 2
ort200
ort029
ort038
ort037
ort036
ort035
ort033
ort030
ort032
ort153
ort464
ort034
ort031
ort154
ort495
ort550
ort261
ort605
ort155
ort454
ort157
ort634
ort512
ort158
ort662
ort590
ort586
ort465
ort535
ort534
ort434
ort352
ort432
ort433
ort204
ort159
ort669
ort548
ort065
ort160
ort268
ort419
ort161
ort476
Pag
5.2920
8.5178
2.8367
1.1663
6.3709
8.4030
7.3539
2.2227
3.6133
4.6848
6.1496
4.6828
1.4946
3.7880
5.2701
5.3987
7.8110
5.1082
9.8678
7.4248
7.7086
2.9645
9.2621
4.0746
7.2425
2.5600
2.5480
4.3429
6.2194
5.9641
6.1640
3.3057
4.9804
6.6264
5.2804
2.3518
3.8947
7.6277
5.8252
8.7134
7.6197
3.1253
7.4376
2.4787
0
0
1
1
0
0
0
1
1
1
0
1
1
1
1
1
0
1
0
0
0
1
0
1
0
1
1
1
0
0
1
1
1
0
0
1
1
0
1
0
0
1
0
1
all0906
all0011
all0010
asl0009
all0008
all0007
all0006
all0005
all0004
alr0786
alr2485
all5038
all5039
asl4181
all4182
alr2083
alr1264
asr4648
alr4650
alr4112
alr2890
alr1890
alr1891
alr5152
alr1543
asl0146
all0147
alr3511
alr3510
alr2268
alr2270
alr2271
alr2272
alr2274
alr0237
alr2980
alr2982
alr2983
all0492
alr4016
alr3705
alr3832
asr3830
alr3829
gll3181
gll2911
gll2910
gsl2909
gll2908
gll2907
gll2906
gll2905
glr4315
gll0557
glr2587
gll2568
gll2570
glr0831
gll0756
glr0827
gll1676
gsl1620
glr1399
gll3732
gll0391
glr2139
glr2136
glr4119
gll3690
gsl0824
gll0825
gll0055
glr2779
glr1916
glr1865
glr1866
glr1867
glr1868
glr2611
glr0782
gll4415
gll1658
gll0663
gll0664
gll4250
glr2652
glr2651
glr3489
Online Supporting Information
1464
1457
1456
1455
1454
1453
1452
1451
1450
1447
1446
1439
1438
1435
1434
1433
1432
1431
1430
1364
1356
1354
1353
1349
1347
1345
1344
1341
1340
1339
1337
1336
1335
1334
1332
1330
1329
1328
1327
1325
1323
1494
1493
1492
1482
1473
1472
1471
1470
1469
1468
1467
1466
1463
1461
1452
1451
1447
1446
1445
1444
1442
1441
1434
1433
1431
1430
1426
1422
1421
1420
1417
1416
1414
1412
1411
1410
1409
1407
1404
1403
1402
1401
0478
1398
1528
1527
1526
372.18
502.192
502.193
502.194
502.195
502.196
502.197
502.198
502.199
478.98
407.12
431.32
431.30
366.9
366.8
388.8
474.52
489.4
489.6
507.171
420.37
507.265
507.266
507.244
477.121
457.24
457.23
504.61
494.77
440.13
440.16
440.17
440.18
440.19
506.152
423.49
423.51
423.52
412.49
412.47
473.95
479.34
479.33
479.32
136.2732
136.2735
136.2736
136.2737
136.2738
136.2739
136.2740
136.2741
136.2742
136.2744
136.2470
131.816
131.815
136.2274
136.2273
128.450
136.2620
135.1706
135.1708
135.1675
133.1324
133.1160
133.1161
135.1971
124.129
124.128
124.127
126.282
126.281
126.231
126.233
126.234
126.235
126.236
124.111
129.572
129.573
129.574
135.1879
136.2769
136.2217
135.1965
135.1964
135.1963
1617
1610
1609
1608
1607
1606
1605
1604
1603
1601
1599
1592
1591
1588
1587
1586
1585
1584
1583
1439
1438
1436
1435
1430
1428
1426
1425
1422
1421
1420
1418
1417
1416
1415
1413
1411
1410
1409
1408
1406
1404
1649
1648
1647
slr0950
sll1321
sll1322
ssl2615
sll1323
sll1324
sll1325
sll1326
sll1327
slr1287
slr1691
slr1330
slr1329
ssr3307
slr1945
sll0368
slr0086
ssl2982
slr0249
sll2010
sll1252
sll1908
sll1909
slr0050
slr0457
ssr2799
slr1678
sll0698
slr1159
slr1226
sll1508
sll1605
sll0379
slr0015
sll2001
slr1915
slr1031
sll0838
sll1973
slr0730
sll1374
slr0744
ssr1238
slr0743
tll1457
tlr0429
tlr0430
tlr0431
tlr0432
tlr0433
tlr0434
tlr0435
tll0385
tlr0672
tlr1180
tlr0526
tlr0525
tsl1100
tlr0151
tll2320
tll2215
tsr2257
tlr1446
tll0073
tlr2161
tlr0325
tlr0326
tll0915
tlr1606
tsl0166
tll0167
tlr0437
tlr1839
tll1496
tlr1790
tlr1791
tlr1792
tll0321
tlr1745
tll2044
tlr0050
tll0395
tll1107
tll1109
tlr1521
tlr1066
tsl1936
tll1937
122.6696
122.6792
122.6793
122.6794
122.6795
122.6796
122.6797
122.6798
122.6801
100.51
119.4282
113.2071
113.2070
121.5186
121.5185
119.4313
114.2287
121.6012
121.6014
121.5853
120.5114
120.4551
120.4552
118.3927
112.1867
121.5643
121.5642
103.322
103.320
122.6948
113.2015
113.2016
113.2017
113.2020
96.8550
122.7672
122.7673
122.7675
119.4099
119.4097
122.6726
120.4723
120.4722
120.4721
0482
0488
0489
0490
0491
0492
0493
0494
0495
0499
0502
0511
0512
0518
0519
0520
0523
0525
0526
0530
0531
0533
0534
0538
0544
0546
0547
0551
0552
0554
0556
0557
0558
0559
0562
0567
0568
0571
0577
0581
0583
0597
0599
0600
232.3375
232.1561
232.1560
232.1559
232.1558
232.1557
232.1556
232.1555
232.1554
232.4447
232.4304
232.1258
232.1259
232.4601
232.4600
232.2042
232.4453
232.986
232.984
232.4668
232.4879
232.2652
232.2653
232.1359
232.3824
232.5365
232.5366
232.2136
232.2137
232.3994
232.3996
232.3997
232.3998
232.3999
232.1665
232.4794
232.4792
232.4791
232.1834
232.670
232.2482
232.843
232.844
232.845
114.290
362.6283
362.6284
362.6285
362.6286
362.6287
362.6288
362.6289
362.6290
211.1101
362.6471
280.2097
280.2096
277.2029
277.2028
362.6742
360.5052
188.857
188.859
312.2770
309.2703
362.6395
362.6396
276.2011
362.6585
345.3730
345.3729
197.946
360.4899
323.3060
323.3062
310.2718
350.3971
350.3972
315.2839
305.2610
362.6746
344.3688
316.2864
316.2862
320.2981
309.2700
309.2699
309.2698
atp1
atpI
atpH
atpG
atpF
atpD
atpA
atpC
nadE
atpE
atpB
pgmI
pyrR
rpoZ
murD
serA
prmA
truB
rpl27
rpl21
nblS
purD
purC
lpxC
fabZ
lpxA
lpxB
tyrS
pyrF
infB
nusA
hemolysin-like protein
possible ATP synthase protein 1
ATP synthase subunit A
ATP synthase subunit c
putative ATP synthase subunit B'
putative ATP synthase B chain
putative ATP synthase delta chain
ATP synthase subunit alpha
ATP synthase subunit gamma
conserved hypothetical protein
putative glutamine dependent NAD(+) synthetase
putative ATP synthase epsilon subunit
ATP synthase beta subunit
conserved hypothetical protein
Phosphoglycerate mutase, co-factor-independent (
possible pyrimidine operon regulatory protein Pyr
putative DnaK-type molecular chaperone (HSP70 fam
putative DNA-directed RNA polymerase (omega c
conserved hypothetical protein
UDP-N-acetylmuramoylalanine--D-glutamate ligase
conserved hypothetical protein
putative D-3-phosphoglycerate dehydrogenase (PG
putative methyltransferase for Ribosomal protein L11
conserved hypothetical protein
putative tRNA pseudouridine 55 synthase
50S ribosomal protein L27
50S ribosomal protein L21
two-component sensor histidine kinase
phosphoribosylglycinamide synthetase
SAICAR synthetase
UDP-3-0-acyl N-acetylglucosamine deacetylase
(3R)-hydroxymyristoyl-[acyl carrier protein] dehydra
UDP-N-acetylglucosamine acyltransferase
Lipid-A-disaccharide synthetase
Leucine aminopeptidase
conserved hypothetical protein
t-RNA synthetase, class Ib:Tyrosyl-tRNA syntheta
orotidine 5'-phosphate decarboxylase
conserved hypothetical membrane protein
conserved hypothetical protein
putative GPH family sugar transporter
translation initiation factor IF-2
conserved hypothetical protein
N utilization substance protein A
Table 2
ort162
ort574
ort623
ort221
ort603
ort604
ort163
ort164
ort165
ort166
ort215
ort378
ort259
ort366
ort315
ort167
ort269
ort168
ort169
ort171
ort514
ort244
ort235
ort256
ort435
ort430
ort172
ort257
ort551
ort522
ort678
ort417
ort677
ort418
ort345
ort329
ort504
ort245
ort649
ort173
ort628
ort301
Pag
8.1709
5.3387
5.5292
5.3360
1.5346
4.5380
4.5235
6.7162
8.9004
5.6156
5.4518
8.6143
5.8338
8.4453
10.6937
5.6269
3.7840
5.6993
8.1606
1.9577
7.5842
4.0773
7.3444
9.2918
3.4978
6.5219
6.2089
3.0754
5.9182
1.9365
5.2305
2.8518
5.6368
4.7731
3.2475
4.7620
5.6864
3.2275
5.4471
8.3490
9.8279
2.8155
0
0
1
0
1
1
0
0
0
0
1
0
0
0
0
1
1
0
0
1
0
1
0
0
1
0
1
1
0
1
0
1
0
0
1
1
1
1
0
0
1
1
alr3828
all0888
asr1592
alr1593
alr1594
alr1596
all0355
alr4537
asr0043
alr0044
alr0045
alr3182
alr0489
alr3724
all0455
all0876
alr0483
asr0485
alr0486
alr0487
alr0488
alr4178
alr4175
alr4174
all3184
alr3185
alr3603
alr3606
alr1798
alr4291
all4289
alr4627
all4752
asl4195
alr4351
all1092
alr1254
all0723
all4120
all4825
all2297
all0152
glr3488
gll0030
gll0160
gll2367
glr2283
glr4278
gll2079
gll3007
gsl2882
gll2881
gll2880
glr0708
gll2595
glr1457
gll0377
gll4186
gll3210
gsr0474
glr0702
glr0703
glr0704
gll0082
gll0084
gll3538
glr0786
gll4414
glr1484
gll2569
glr3587
glr2324
glr0079
gll1136
glr3257
gsr0413
gll2252
glr0851
gll0636
gll3233
gll4295
glr0759
gll3300
glr1714
Online Supporting Information
1491
1489
1487
1486
1485
1483
1481
1480
1479
1478
1477
1475
1467
1466
0389
0390
0391
0393
0394
0395
0396
0397
0398
0399
0400
0401
0403
0405
0406
1158
1156
1154
1152
1151
1142
1141
1140
1138
1051
1053
1054
1055
1525
1511
1509
1508
1507
1505
1503
1501
1500
1499
1498
1496
1487
1485
0198
0202
0203
0205
0206
0207
0208
0209
0211
0212
0213
0214
0216
0220
0223
1180
1178
1176
1173
1169
1161
1159
1157
1155
1143
1138
1136
1135
479.31
477.48
498.42
498.43
498.45
498.47
452.61
475.111
506.99
506.100
506.101
458.52
468.88
508.101
461.19
463.41
468.80
468.83
468.84
468.86
468.87
366.14
366.12
353.8
420.44
420.14
344.2
344.3
489.32
496.2
504.113
478.2
505.118
374.33
501.168
452.54
429.46
483.89
474.32
484.89
481.38
506.268
135.1962
136.2210
133.1331
133.1332
133.1333
133.1335
135.2105
135.2108
135.2109
135.2110
135.2111
136.2702
128.481
134.1466
135.1782
136.2712
131.831
135.1936
135.1937
135.1938
135.1939
134.1494
134.1492
134.1491
131.882
131.840
126.228
134.1548
131.837
127.382
127.321
125.201
125.164
129.543
133.1327
135.2148
136.2425
136.2854
135.1892
128.440
132.1098
136.2868
1646
1644
1642
1641
1640
1638
1636
1634
1633
1632
1631
1629
1621
1620
0386
0387
0388
0390
0391
0392
0393
0394
0395
0396
0397
0398
0400
0401
0402
1255
1253
1251
1248
1246
1236
1235
1234
1232
1150
1148
1147
1146
slr0742
slr0194
ssl2233
sll1786
sll1787
sll1789
sll0098
slr1098
ssl1263
sll0661
sll0662
slr0072
slr0451
slr0018
slr1879
slr1896
slr1974
ssl0105
slr0556
slr2073
slr0661
slr1508
slr0181
sll1776
sll0947
slr0994
slr1600
sll1841
sll0467
sll0851
sll0226
sll0065
slr0399
ssl3441
sll0019
slr0958
slr0707
sll0245
sll0455
sll1643
sll0896
slr1030
tll1938
tll1273
tsl1188
tll1187
tll0642
tll0640
tll2425
tll0329
tsr2138
tlr2139
tlr2140
tll1704
tlr0350
tll1534
tlr1449
tlr1934
tlr0878
tsl1609
tll1037
tlr1216
tlr1217
tll0327
tlr2234
tlr1079
tlr0833
tll0832
tll1300
tll1299
tll0922
tlr1631
tll1388
tll0880
tll0859
tsr0101
tlr1040
tlr1827
tll1339
tll1587
tll0277
tll0980
tlr1137
tll1511
120.4719
93.8368
100.36
100.37
100.38
100.40
100.17
121.5533
122.6509
122.6510
122.6511
117.3500
100.53
112.1819
118.3831
104.409
116.2932
122.6868
122.6870
122.6874
122.6875
122.7159
122.7155
122.7154
95.8470
95.8463
115.2573
115.2574
118.3847
122.7730
122.6413
115.2593
95.8445
99.8787
116.3018
120.4696
122.7460
121.5444
122.7038
119.4298
119.4463
119.4459
0601
0609
0611
0612
0613
0615
0617
0621
0622
0623
0624
0626
0636
0637
0653
0656
0657
0659
0660
0661
0662
0663
0665
0666
0667
0668
0670
0671
0672
0676
0678
0680
0683
0686
0698
0701
0702
0704
0711
0714
0715
0716
232.846
232.3355
232.3075
232.3076
232.3077
232.3079
232.1739
232.5257
232.1586
232.1587
232.1588
232.2767
232.1829
232.2455
232.1797
232.3344
232.1824
232.5570
232.1826
232.1827
232.1828
232.4604
232.4606
232.4607
232.2769
232.2770
232.2085
232.2087
232.3656
232.5100
232.5098
232.1006
232.894
232.4587
232.5157
232.2612
232.4462
232.3483
232.4658
232.1066
232.4017
232.5369
309.2697
265.1827
350.3956
350.3957
350.3958
350.3959
361.5814
357.4428
291.2286
291.2287
291.2288
330.3242
361.5896
206.1050
362.6590
82.141
356.4254
361.5817
361.5818
359.4834
359.4835
338.3506
202.1004
282.2125
362.6160
362.6612
361.5438
335.3423
300.2486
83.143
362.6489
359.4703
69.88
296.2398
358.4480
356.4250
332.3308
336.3426
362.6617
103.241
361.5674
362.6292
conserved hypothetical protein
cbbI,
rpiA,
ppi
rpsT
rpoB
rpoC2
ycf35
gidB
fumC
cobI
proC
lrtA
lipB
queA
psbC
ycf4
ilvN
ycf39
infA
dxr
cysRS
polA
thrA
ruvC
chlI
putative ribose 5-phosphate isomerase A
30S ribosomal protein S20
possible deoxyribonuclease similar to TatD
DNA-directed RNA polymerase beta chain
RNA polymerase beta prime subunit
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
possible 3Fe-4S ferredoxin
putative glucose inhibited division protein B
putative DNA helicase
Fumarate hydratase
PRECORRIN-2 C20-METHYLTRANSFERASE
conserved hypothetical protein
putative GTP-binding protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
putative pyrroline-5-carboxylate reductase
probable glycosyltransferase
possible Recombination protein O (RecO)
Putative deoxyribose-phosphate aldolase
light repressed protein A homolog
putative lipoate-protein ligase B
conserved hypothetical protein
Putative dihydrolipoamide acetyltransferase comp
Queuosine biosynthesis protein
photosystem II chlorophyll-binding protein CP43
photosystem I assembly protein (Ycf4 family)
Acetolactate synthase small subunit
putative chaperon-like protein for quinone binding in
translation initiation factor IF-1
1-deoxy-D-xylulose 5-phosphate reductoisomerase
cysteinyl-tRNA synthetase
DNA polymerase I
probable GTP-binding protein
homoserine dehydrogenase
conserved hypothetical protein
Holliday junction resolvase RuvC
Protoporphyrin IX Magnesium-chelatase subunit
Table 2
Pag
ort249
ort330
ort491
ort175
ort409
ort663
ort395
ort396
ort176
ort425
ort357
ort324
ort045
ort682
ort492
ort496
ort405
ort178
ort179
ort180
ort181
ort513
ort426
ort004
6.2356
6.5083
2.2649
8.0009
7.5469
2.0190
1.7450
2.9578
6.3910
2.5893
4.6210
4.4641
6.8123
4.2712
3.5522
8.8654
5.7866
8.2150
7.9997
8.5324
10.3178
6.4096
3.7672
3.6739
0
0
1
0
0
1
1
1
0
1
0
1
0
1
1
0
0
0
0
1
0
0
1
1
alr4542
all1365
asr1366
all1367
all1368
alr0052
alr0051
all0860
alr2450
alr4840
alr0212
alr0213
alr3934
all4019
all4121
all4063
all4506
all2716
alr3100
alr3101
alr3102
alr3103
alr1313
all2364
glr2140
gll2782
gsl0511
gll2930
glr0407
gll0880
glr1603
gll3082
glr4151
gll2290
gll1884
gll0416
glr3695
glr3178
gll2295
glr0301
glr0706
glr0793
gll1132
gll1131
gll1129
gll0069
gll3551
glr1605
1056
1057
1058
1059
1060
1061
1062
1063
1065
1066
1069
1070
1072
1074
1075
0798
0796
0794
0791
0790
0789
0788
0786
0784
1132
1131
1130
1129
1128
1127
1126
1124
1122
1121
1110
1109
1104
1102
1101
0518
0520
0523
0526
0527
0528
0529
0531
0534
348.20
498.50
498.112
498.49
498.48
493.78
493.77
424.29
506.176
505.188
504.198
504.199
505.210
507.156
474.31
508.85
455.50
466.40
509.282
509.283
509.285
509.286
497.43
497.48
135.1633
133.1173
133.1310
133.1172
133.1171
135.2074
135.2073
136.2694
135.2041
133.1210
132.1115
132.1116
135.1784
131.893
134.1488
135.1770
135.1773
129.593
125.183
125.184
125.185
130.682
133.1159
135.1833
1144
1143
1142
1141
1140
1139
1138
1137
1135
1134
1130
1129
1126
1124
1123
0874
0872
0870
0867
0866
0865
0864
0862
0859
slr0120
sll1245
smr0010
slr0383
slr0084
slr0623
slr1722
slr0417
sll0735
slr0186
sll0753
slr0739
sll1501
slr1843
slr1643
sll1522
slr0652
slr1796
sll1547
sll1109
slr0362
slr2035
slr1517
sll0336
tll2116
tll2429
tsr0877
tlr1053
tlr1536
tll0812
tll2190
tlr1369
tll1974
tll1397
tll0021
tll0020
tlr1848
tll0540
tlr1211
tll1275
tll0216
tlr1421
tll2329
tll1867
tll0495
tll2118
tlr1600
tlr1643
120.4823
109.1123
109.1189
109.1121
109.1120
113.2011
113.2003
120.5100
122.7759
122.6760
120.5087
120.5088
122.7733
118.3670
119.4027
116.2896
121.5431
121.5725
117.3230
117.3232
117.3234
110.1319
117.3435
122.6621
0719
0720
0721
0722
0723
0724
0725
0727
0729
0730
0740
0742
0748
0750
0751
0771
0773
0776
0779
0780
0781
0782
0784
0788
232.5260
232.2899
232.5612
232.2898
232.2897
232.1595
232.1594
232.3329
232.4270
232.1082
232.1641
232.1642
232.748
232.666
232.4657
232.628
232.2276
232.3153
232.2694
232.2695
232.2696
232.2697
232.1911
232.4084
310.2722
361.5608
361.5636
339.3528
362.6518
207.1057
359.4808
321.3012
340.3569
276.2012
361.5626
268.1877
76.122
324.3080
343.3658
357.4422
362.6327
212.1113
292.2320
300.2498
71.95
324.3087
361.5260
362.6124
ort044
ort542
ort182
ort332
ort300
ort359
2.1308
4.5633
5.4837
3.6056
2.4003
8.2432
1
0
0
1
1
0
all4563
alr2475
asr2474
alr2542
all4365
alr4386
gll0752
glr1325
gsl0442
gll1206
gll2622
glr0540
0781
0780
0779
0832
0831
0830
0537
0539
0540
0814
0815
0816
493.70
465.67
465.66
498.2
440.25
501.135
133.1293
132.1010
132.1009
130.766
130.649
131.808
0855
0854
0853
0904
0903
0902
sll0018
slr0520
slr0519
sll1058
slr1055
slr2026
tlr0376
tlr2187
tsr2185
tll1987
tlr0271
tlr1522
120.4621
110.1374
110.1373
119.3993
121.5660
112.1727
0791
0793
0794
0819
0820
0822
232.1445
232.4294
232.4293
232.4360
232.2217
232.2195
332.3318
362.6487
362.6486
360.4914
357.4373
205.1038
ort654
ort057
ort183
ort043
ort184
ort185
ort367
ort197
ort061
ort187
ort485
4.8826
6.1935
8.0607
3.3436
6.4854
4.9317
4.8449
3.0645
5.3822
7.2858
4.6257
1
0
0
1
1
1
0
1
0
0
0
alr4385
all0640
alr4979
alr3809
alr4169
alr4171
all1691
alr0799
asr0798
all4869
all0218
gll1040
gll2329
gll3597
gll1769
gsl0787
gll2939
glr3304
glr3340
gsr4417
gll3437
gll0103
0829
0827
1170
0825
0823
0821
0637
1111
1110
1109
1107
0817
0819
0821
0822
0824
0825
0858
1095
1094
1093
1091
501.134
479.58
399.18
479.11
353.3
353.5
463.18
443.28
443.27
443.26
504.10
128.519
136.2606
136.2554
121.7
136.2648
136.2650
134.1479
134.1390
134.1389
124.110
124.118
0901
0899
1181
0897
0895
0893
0794
1085
1086
1087
1089
slr0783
sll1276
slr1900
sll0370
slr1886
sll0585
sll0567
slr1846
ssr3122
slr1160
slr1779
tlr0966
tlr0962
tll0916
tll2332
tlr1222
tll1062
tll0048
tll0874
tsl0875
tll0135
tlr0838
112.1726
120.5139
113.2078
104.406
122.7175
122.7177
110.1378
118.3891
118.3890
118.3889
120.4563
0823
0825
0829
0830
0832
0834
0865
0906
0907
0908
0910
232.2196
232.3432
232.1217
232.868
232.4612
232.4610
232.5028
232.4471
232.4470
232.1108
232.1647
205.1037
321.3002
128.365
361.5742
359.4813
359.4815
360.4935
247.1570
247.1569
224.1263
324.3095
Online Supporting Information
cytM
petG
hisH
trxA
guaB
gyrA
leuA
folD
crtE
cbiA
zwf
petH
pgsA
hisA
proB
leuB
accD
cbbA,
cfxA,
fbaA,
fda
purQ
dapB
chlH
folP
cbbJ,
tpiA
carB
fur
pdxJ
probable tRNA/rRNA methyltransferase
cytochrome cM
Cytochrome b6f complex subunit 5
conserved hypothetical protein
Glutamine amidotransferase class-I
Thioredoxin
putative IMP dehydrogenase
DNA gyrase A subunit
conserved hypothetical protein
2-isopropylmalate synthase
methylenetetrahydrofolate dehydrogenase
geranylgeranyl pyrophosphate synthase
putative Cobyrinic acid a,c-diamide synthase
glucose-6-phosphate dehydrogenase
ferredoxin--NADP reductase (FNR)
CDP-diacylglycerol-glycerol-3-phosphate 3-phosphat
phosphoribosylformimino-5-aminoimidazole carboxa
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
putative glutamate 5-kinase
3-isopropylmalate dehydrogenase
acetyl-CoA carboxylase, beta subunit
Fructose-bisphosphate/sedoheptulose-1,7-bisphosp
phosphoribosylformylglycinamidine synthase
conserved hypothetical protein
dihydrodipicolinate reductase
Protoporphyrin IX Magnesium chelatase subunit c
putative dihydropteroate synthase
triosephosphate isomerase
ABC transporter, possibly multidrug efflux
conserved hypothetical protein
carbamoyl phosphate synthetase, large subunit
conserved hypothetical protein
conserved hypothetical protein
Ferric uptake regulator family
glutaredoxin-like protein
BolA family protein
conserved hypothetical protein
Pyridoxal phosphate biosynthetic protein PdxJ
Table 2
ort049
ort560
ort039
ort671
ort188
ort436
ort282
ort305
ort265
ort280
ort041
ort625
ort440
ort423
ort266
ort456
ort381
ort066
ort020
ort242
ort233
ort458
ort629
ort006
ort056
ort067
ort042
ort068
ort239
ort370
ort339
ort069
ort611
ort340
ort283
ort422
ort631
ort632
ort070
ort382
ort192
ort273
ort071
ort072
Pag
4.8613
2.5127
8.9380
5.3414
5.7140
4.9091
8.8799
0.9607
6.6372
5.4243
9.1914
7.0924
7.6179
2.0589
3.9430
7.9238
6.0105
7.6070
11.5504
5.6520
3.6327
7.6720
4.3042
3.0815
6.0807
7.5864
4.3204
8.0286
5.1483
4.1255
3.3715
8.5950
4.3506
5.6077
6.2624
7.2306
4.1149
6.9207
7.1654
2.7930
6.0516
8.8208
9.2089
5.9052
1
1
0
0
1
1
0
1
0
0
0
0
0
1
0
0
0
0
0
0
1
0
1
1
0
0
1
0
0
1
1
0
1
0
0
0
1
0
0
1
0
0
0
0
all2146
alr4977
alr1921
all2995
all2996
all2997
alr2998
alr2999
alr2764
all3875
all4887
all3873
alr3871
alr4670
alr1879
all0036
alr3921
alr3919
all5019
all2568
alr2001
alr0094
alr0096
all4257
alr4715
asl1962
alr1155
alr1158
alr1159
all1053
all3578
all0748
asl0749
all1323
alr3229
alr3230
all0121
all0120
alr3655
alr2328
all4872
alr4577
alr4576
asl2557
gll4135
glr3499
glr4328
gll0108
gll0109
gll0110
glr2063
glr2064
gll1456
gll1396
gll3487
glr4397
gll3316
gll0901
glr0932
glr2398
glr0443
gll1313
gll1038
gll2974
glr2943
gll1496
gll0753
gll0159
gll3672
gsl3751
gll3543
glr4180
glr4181
gll1528
glr3934
glr1740
gsl4026
gll4083
gll1991
gll0102
glr4166
glr4167
glr2407
glr1052
gll1053
glr0072
glr4030
gsr1914
Online Supporting Information
1099
1097
1093
1092
1091
1090
1089
1088
1087
1085
1084
0658
1081
1080
0609
0610
0611
0612
0613
0614
0615
0617
0618
0619
0954
0953
0951
0949
0948
0946
0945
0944
0943
0939
0933
0932
0929
0928
0923
0920
0918
0915
0914
0744
1080
1077
1056
1057
1058
1059
1060
1061
1062
1065
1066
1069
1071
1074
0403
0401
0400
0399
0398
0396
0395
0393
0392
0389
0655
1037
0653
0651
0650
0648
0647
0646
0645
0641
0621
0620
0617
0616
0607
0601
0599
0595
0594
0593
474.91
505.41
479.62
489.65
489.64
489.62
489.55
489.56
492.34
432.43
506.205
432.44
432.17
422.30
402.16
505.89
460.13
460.10
480.22
441.45
493.79
444.48
436.4
462.4
505.57
466.22
477.2
477.5
477.6
480.85
502.210
472.34
472.33
466.16
502.1
502.2
370.26
370.27
430.13
481.19
443.24
430.2
430.1
494.69
135.1906
133.1251
136.2305
136.2700
136.2699
136.2698
136.2385
136.2386
131.915
136.2320
127.299
134.1463
134.1505
130.641
129.604
135.2066
136.2373
135.1823
136.2402
136.2557
131.841
131.844
131.845
128.472
127.373
131.819
130.776
130.778
130.779
130.781
130.734
131.805
131.804
128.497
136.2363
136.2364
136.2451
136.2452
133.1196
130.757
135.1785
135.2122
135.2121
124.120
1096
1098
1102
1103
1104
1105
1106
1107
1108
1111
1112
1114
1116
1118
1052
1051
1050
1049
1048
1046
1045
1043
1042
1041
0742
0743
0745
0747
0748
0750
0751
0752
0753
0757
0763
0764
0767
0768
0774
1038
1036
1032
1031
1030
slr2019
slr1426
slr1364
sll0506
sll0505
sll0504
slr0853
sll0020
slr1167
slr1369
sll1683
slr0361
sll1676
sll0469
sll0945
slr1351
sll0899
sll0983
slr0444
slr1718
sll0601
slr1746
slr0611
sll0542
slr0615
ssr2551
sll1498
slr0954
slr0955
slr0877
slr0603
sll0933
ssl1784
sll1868
sll0708
sll0711
slr0774
slr0775
sll1968
slr1756
sll1631
slr1366
slr1365
ssl3451
tlr0577
tll2204
tll0661
tlr1763
tlr1762
tlr1761
tll0471
tll0307
tll2051
tll2108
tlr1866
tlr0656
tlr0708
tlr1546
tll0763
tlr1553
tlr0393
tll1622
tlr0343
tll0403
tll0920
tlr0461
tlr1757
tll0887
tlr0655
tsr1432
tll0760
tlr0428
tll1042
tll1003
tll2056
tlr1208
tsr1207
tlr1317
tlr0659
tll0500
tll0203
tll0202
tlr1461
tll1588
tlr0177
tlr2420
tll0901
tsl2428
116.3092
103.384
106.684
98.8680
98.8679
98.8675
98.8733
98.8735
121.6207
112.1671
119.4089
112.1672
112.1842
118.3586
109.1118
122.6421
122.6680
122.6679
122.7271
80.8040
116.2875
121.6057
121.5331
115.2420
117.3434
121.5982
112.1859
112.1862
112.1863
114.2352
119.4212
121.5340
121.5339
118.3845
118.3872
122.6913
97.8587
97.8588
122.7363
122.7439
120.5015
106.687
106.686
104.417
0924
0928
0933
0934
0935
0936
0937
0938
0939
0942
0944
0949
0962
0966
1000
1002
1003
1004
1005
1007
1008
1010
1011
1013
1023
1024
1026
1028
1029
1031
1032
1033
1034
1038
1052
1053
1056
1057
1068
1073
1076
1079
1080
1081
232.1937
232.1215
232.3256
232.4781
232.4780
232.4779
232.4778
232.4777
232.3920
232.796
232.1126
232.798
232.800
232.965
232.3630
232.1578
232.756
232.758
232.1221
232.4381
232.3898
232.5318
232.5319
232.5064
232.927
232.3218
232.3277
232.3279
232.3280
232.2640
232.5452
232.3508
232.3509
232.2681
232.3733
232.3734
232.5340
232.5339
232.2531
232.4048
232.1111
232.1430
232.1431
232.4371
281.2107
359.4760
360.4910
356.4269
356.4268
356.4267
268.1879
361.5366
356.4294
312.2764
268.1880
362.6561
362.6305
337.3476
227.1297
353.4119
362.6644
360.4985
129.373
360.5038
353.4111
360.5050
360.5051
361.5663
329.3227
340.3568
360.5089
301.2517
301.2518
330.3245
358.4486
270.1913
362.6736
260.1755
320.2971
295.2379
352.4038
352.4039
309.2711
361.5271
342.3652
360.4912
360.4911
231.1346
recR
bioB
uppS
lysA
clpC
cad
rsuA
malQ
kprS
murF
glmU
aroA
murI
sds
acs
carA
gatA
dnaE
rps15
dnaG
ispE
secD
secF
glnA
ABC transporter, multidrug efflux family
RecR protein
biotin synthase
Undecaprenyl pyrophosphate synthetase (UPPS)
conserved hypothetical protein
diaminopimelate decarboxylase
putative ribosomal-protein-alanine acetyltransferase
endopeptidase Clp ATP-binding chain C
putative glycerol dehydrogenase
putative phosphatidate cytidylyltransferase
Orn/Lys/Arg decarboxylases family 1
putative pseudouridylate synthase specific to ribosom
Putative 4-alpha-glucanotransferase
Ribose-phosphate pyrophosphokinase
Putative glycogen synthase (glgA)
Cytoplasmic peptidoglycan synthetases, N-terminal:C
UDP-N-acetylglucosamine pyrophosphorylase
conserved hypothetical protein
EPSP synthase (3-phosphoshikimate 1-carboxyvinyltr
probable 2-phosphosulfolactate phosphatase
Possible nitrilase
Putative Aspartate and glutamate racemases:Glutamat
polyprenyl synthetase; solanesyl diphosphate synth
acetyl-coenzyme A synthetase
ABC transporter, multidrug efflux family
conserved hypothetical protein
carbamoyl-phosphate synthase small chain
conserved hypothetical protein
possible tRNA/rRNA methyltransferase
glutamyl-tRNA (Gln) amidotransferase subunit A
DNA polymerase III, alpha subunit
conserved hypothetical protein
30S ribosomal protein S15
putative DNA primase
putative rRNA (adenine-N6,N6)-dimethyltransferase
Putative 4-diphosphocytidyl-2C-methyl-D-erythritol k
preprotein translocase subunit
preprotein translocase subunit
conserved hypothetical protein
Glutamine synthetase, glutamate--ammonia ligase
cytidine/deoxycytidylate deaminase family protein
putative lipoprotein signal peptidase
conserved hypothetical protein
conserved hypothetical protein
Table 2
ort482
ort225
ort616
ort664
ort558
ort255
ort637
ort390
ort304
ort667
ort217
ort226
Pag
7.5546
4.3031
2.2408
3.2377
5.5049
7.1035
4.7762
7.9863
2.1261
1.9233
4.7233
4.3761
0
0
1
1
0
0
1
0
1
1
0
1
alr3707
all4793
all4792
all4791
all4789
all4116
alr1348
alr4111
alr0128
all4140
alr4068
all0936
glr2589
gll2797
gll1830
gll1829
gll1278
gll1805
glr1848
glr1646
glr4377
gll1520
glr3264
glr2022
0747
0752
0753
0754
0756
0757
0758
0759
0760
0762
0764
0765
0590
0585
0584
0583
0581
0580
0579
0578
0577
0575
0572
0570
493.86
493.62
493.94
493.95
493.98
506.66
448.44
507.170
504.170
389.23
477.41
501.67
124.87
135.1925
129.552
129.553
134.1552
136.2795
136.2582
136.2522
136.2326
133.1336
136.2245
136.2247
0819
0824
0825
0826
0828
0829
0830
0831
0832
0834
0836
0838
slr0116
sll1664
sll1260
sll1261
slr0020
slr1679
slr0963
slr0220
sll1091
slr1105
slr0251
sll1513
tll2308
tll0992
tll1688
tll1687
tll0735
tll2463
tlr0339
tll2192
tll0150
tlr2283
tll1571
tlr1615
120.5073
114.2275
101.96
101.97
101.99
122.6782
88.8199
121.5852
115.2471
122.7918
122.6747
118.3622
1084
1089
1090
1091
1093
1094
1095
1096
1097
1109
1112
1114
232.2484
232.1035
232.1032
232.1031
232.1029
232.4662
232.3880
232.4669
232.5347
232.4639
232.623
232.4396
311.2748
231.1344
355.4199
355.4200
257.1720
234.1382
329.3229
349.3913
225.1268
361.5888
324.3103
289.2253
ort573
5.0177
1
alr0782
gll3548
0766
0569
464.41
127.350
0839
sll0807
tll2369
122.6539
1115
232.3533
359.4803
ort384
ort398
ort008
ort391
ort251
ort287
ort322
ort510
ort073
ort074
ort075
ort076
ort027
ort373
ort062
ort292
ort354
ort681
ort077
ort594
ort655
ort286
ort321
ort078
ort443
ort248
ort613
ort595
2.9450
4.9077
3.3229
4.5135
9.5890
7.1471
5.6617
3.2001
10.1062
4.6868
11.1679
6.2868
5.8281
2.2365
4.7740
3.9710
6.5069
9.0545
7.3219
3.7495
2.5827
5.8235
8.1273
7.7510
5.2283
8.5050
1.7582
2.0761
1
1
1
1
0
0
0
1
0
0
0
1
0
1
1
1
0
0
0
1
0
0
0
0
0
0
1
1
alr1041
alr1042
all4645
alr5275
alr1602
all2063
all3392
all4379
all3259
alr2014
alr1349
alr1612
alr4853
all2501
all2500
all5215
alr3460
alr1240
alr5129
asl3674
alr4641
alr3352
all3174
all3821
all0233
all4450
asl4451
asl4452
glr3342
glr1218
gll4260
gll1117
glr3180
gll0063
gll0123
glr3159
glr1039
glr1395
gll4381
gll0900
glr2600
gll3622
gll3102
gll3837
glr1831
gll1448
glr0972
gsl0792
gll3158
gll0699
glr0747
gll4313
gll3023
gll1616
gsl3059
gsl3060
0767
0768
0769
0770
0771
0776
0778
0663
0664
0667
0668
0669
0674
0676
0677
0839
0841
0847
0850
0853
0856
0862
0863
0865
0867
0868
0869
0870
0568
0567
0566
0565
0564
0558
0556
0791
0789
0787
0786
0785
0779
0777
0776
0775
0772
0766
0763
0757
0754
0750
0749
0745
0743
0741
0740
0739
443.51
443.53
457.46
506.7
397.26
454.26
400.30
370.7
505.36
458.41
448.46
430.23
450.3
492.100
492.102
493.138
504.126
462.61
435.38
448.15
346.9
346.5
405.44
479.120
506.108
498.149
498.147
498.146
136.2249
136.2250
127.345
136.2594
136.2837
135.2130
132.1090
131.846
136.2857
136.2859
132.1000
136.2387
129.557
121.2
121.3
128.454
135.1910
135.2024
136.2872
134.1472
131.905
135.2052
134.1476
135.2145
134.1587
134.1578
134.1577
134.1576
0840
0841
0842
0843
0844
0849
0851
1029
1028
1025
1024
1023
1018
1015
1014
1000
0997
0988
0985
0981
0978
0975
0974
0972
0970
0969
0968
0967
slr2094
slr1808
slr1176
sll0329
sll1479
sll1035
slr0502
slr1228
slr1918
slr1195
slr0722
sll0875
sll0402
slr2136
slr1751
sll0377
slr0070
sll1910
slr0022
ssr1736
sll0755
slr0992
slr0216
slr0948
slr0649
sll1290
ssr1399
ssr1398
tll1276
tll1738
tlr1287
tlr0576
tlr1076
tlr1764
tll1624
tll2205
tlr2348
tlr0208
tlr1746
tlr2384
tll2357
tlr0996
tll1406
tll0952
tlr1874
tlr1873
tlr0653
tsr1915
tll1454
tlr1793
tll1104
tll0685
tlr0750
tlr0652
tsr2061
tsr2060
119.4322
119.4324
117.3427
115.2577
122.6404
109.1072
108.883
104.464
113.2047
121.5979
88.8200
94.8421
116.2825
121.5491
121.5498
111.1522
111.1641
122.6355
112.1656
118.3703
113.1974
113.1971
121.5389
119.4163
115.2487
121.5958
121.5957
121.5956
1116
1117
1118
1119
1120
1125
1127
1149
1152
1155
1156
1158
1171
1174
1175
1177
1195
1202
1205
1210
1213
1215
1216
1220
1222
1224
1225
1226
232.2593
232.2595
232.991
232.1480
232.3085
232.2026
232.2310
232.2204
232.3759
232.3911
232.3879
232.3093
232.1098
232.4319
232.4318
232.1703
232.2384
232.4430
232.1333
232.2512
232.995
232.2105
232.2759
232.854
232.1661
232.5178
232.5177
232.5176
345.3766
352.4040
221.1219
339.3533
314.2823
326.3147
357.4366
362.6535
305.2620
211.1104
223.1242
255.1691
286.2196
197.949
359.4789
360.4970
205.1044
265.1835
345.3746
233.1376
327.3165
315.2859
313.2790
86.156
361.5541
284.2160
284.2159
284.2158
Online Supporting Information
pcyA
rps2
tsf
recG
sir
glyS
chlP
typA
cbbE,
rpe,
ppE
cbbF,
glpX,
fbp
hemA
agp
gnd
cobW
prfC
aspC
gcpE
fmt
zam
rpl32
tpx
cobU
metG
rps18
rpl33
ferredoxin-dependent biliverdin reductase
possible glycosyltransferase
30S ribosomal protein S2
putative elongation factor EF-Ts
ATP-dependent DNA helicase
putative d-alanyl-d-alanine dipeptidase
Ferredoxin-sulfite reductase
putative Glycyl-tRNA synthetase, beta subunit
geranylgeranyl hydrogenase
tyrosine binding protein
possible ABC transporter, ATP-binding component
possible heme transporter
ribulose-5-phosphate 3-epimerase
Fructose-1,6-bisphosphatase/sedoheptulose-1,7-bis
Possible glutamyl-tRNA reductase
ADP-glucose pyrophosphorylase
6-phosphogluconate dehydrogenase
Putative 6-phosphogluconolactonase, Pgl, DevB
putative uracil phosphoribosyltransferase
putative cobalamin synthesis protein
peptide-chain-release factor RF-3
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
Aminotransferases class-I
GcpE protein
carboxyl-terminal processing protease
Transcriptional-repair coupling factor
putative methionyl-tRNA formyltransferase
putative acetazolamide conferring resistance protein Z
conserved hypothetical protein
50S ribosomal protein L32
thioredoxin peroxidase
putative tRNA/rRNA methyltransferase (SpoU family
putative cobinamide kinase
conserved hypothetical protein
putative methionyl-tRNA synthetase
probable ribonuclease II
30S ribosomal protein S18
50S ribosomal protein L33
Table 2
ort499
ort318
ort674
ort309
ort333
ort428
ort493
ort541
ort013
ort561
ort246
ort079
ort490
ort203
ort413
ort591
ort058
ort080
ort081
ort346
ort082
ort064
ort544
ort083
ort538
ort021
ort084
ort085
ort461
ort086
ort262
ort660
ort264
ort650
ort355
ort088
ort379
ort400
ort089
ort410
ort090
ort338
ort276
ort220
Pag
6.5051
5.6170
4.3774
5.0622
7.0569
4.3385
9.9771
6.2372
4.8173
3.9281
4.6797
5.8593
4.6015
5.9978
4.3030
3.5379
5.9866
7.6393
6.8549
2.5721
5.5161
4.7155
3.7078
8.4322
7.3409
11.5504
9.1356
4.6858
4.0298
7.1266
8.2632
3.5967
7.6843
7.2256
9.4604
8.8310
3.4350
3.1599
7.2057
3.5568
9.0366
3.6201
5.1709
5.6858
0
0
1
1
0
1
0
0
0
1
1
0
1
0
1
1
0
0
0
1
0
1
1
0
0
0
0
0
1
0
0
1
0
1
0
0
1
1
0
1
0
1
1
0
alr4958
alr1689
alr2728
alr4700
alr2048
alr3283
alr1050
all0788
alr3537
all3536
alr4054
alr2431
all2919
all2917
alr2323
asl2630
all2556
all4508
asl4507
alr0599
all5166
asl2061
all4008
all0646
alr2742
alr1924
alr3357
all2545
all4673
alr2751
all3970
all1269
alr2973
alr0346
alr3512
alr2762
all0713
all3909
all3908
all3263
alr4810
alr2009
alr1978
alr1965
gll2926
glr3076
gll3592
glr0847
gll0815
gll4081
gll1692
glr1401
glr4010
glr0988
gll2424
glr1664
gll3182
glr1322
glr1814
gsr3838
glr3389
glr1876
gsl4025
gll0194
glr1858
gsr3540
gll3495
glr1400
gll1252
glr2513
gll2384
gll4395
gll0192
gll3484
gll0656
glr3011
gll1169
gll1127
glr1487
gll4416
glr1306
gll3877
glr2049
glr1211
gsr3242
gll1473
gll2868
glr3383
Online Supporting Information
0871
0879
0882
0884
0888
0889
0890
0891
0892
0893
0301
0895
0898
0899
0901
0902
0903
0904
0905
0907
0909
0910
0912
0741
0683
0682
0681
0680
0678
0801
0802
0598
0596
0595
0591
0588
0584
0583
0582
0578
0571
0565
0561
0560
0738
0727
0724
0722
0716
0715
0714
0710
0709
0708
1900
0705
2195
0699
0696
0695
1012
0689
0688
0685
0683
0682
0679
0675
0669
0667
0666
0665
0661
0506
0504
0422
0425
0426
0435
0439
0444
0445
0446
0453
0466
1187
1192
1193
476.101
463.61
452.22
452.25
507.259
505.68
443.58
490.7
484.106
484.30
393.18
489.37
477.92
477.94
484.114
484.115
494.70
455.48
455.49
458.24
498.70
454.28
412.28
378.2
505.195
479.63
498.37
498.172
382.10
506.145
357.12
492.55
492.50
348.5
452.71
492.31
459.48
508.90
508.91
505.33
415.4
415.9
421.26
483.32
128.496
136.2474
135.2008
135.1973
135.1813
135.2019
135.1867
126.262
133.1289
133.1201
126.283
136.2549
136.2552
136.2553
135.2084
136.2514
127.327
133.1148
126.285
136.2793
136.2300
136.2269
136.2473
133.1358
133.1286
136.2238
134.1564
134.1427
133.1295
136.2253
136.2290
128.444
136.2677
133.1194
136.2595
135.2095
134.1559
134.1560
134.1561
135.1979
136.2308
134.1419
132.1111
132.1110
0966
0957
0954
0952
0948
0947
0946
0945
0944
0943
0332
0940
0993
0937
0934
0933
0932
0931
0930
0928
0926
0925
0923
0919
1008
1009
1010
1011
1013
0879
0880
1063
1065
1066
1070
1074
1078
1079
1080
0582
0573
0567
0563
0562
sll1553
slr1211
sll0865
slr0847
slr1665
sll1074
slr1349
slr0477
sll0080
sll1894
sll0135
sll0860
sll1382
sll1383
sll0430
ssr1604
sll0221
sll0608
sll0609
sll1945
slr1577
ssr2142
sll1275
sll1414
sll0578
slr2130
slr0351
sll1071
sll0622
sll1218
slr1822
slr1884
sll0593
sll1760
slr1626
sll1702
sll0158
slr0536
sll0456
slr0608
slr0815
sll0848
slr1149
sll0900
tll0662
tlr0900
tlr1753
tlr1165
tll2294
tll2098
tll0717
tlr2326
tll2219
tlr1727
tlr1281
tll0315
tlr1656
tlr1657
tll1191
tlr2462
tlr1194
tlr1437
tsr2284
tll0623
tlr0846
tsr0534
tll2275
tlr1134
tlr1258
tlr0784
tlr0417
tlr0249
tll0231
tll1029
tll1641
tlr1996
tll1495
tlr1765
tll0747
tll1092
tll0578
tlr0741
tlr0742
tll0233
tlr0707
tlr0603
tll0559
tll0180
114.2139
121.6082
113.1949
122.7854
101.164
111.1482
120.4957
122.6973
121.5234
122.6257
119.4415
116.2789
118.3729
118.3731
120.4595
120.4598
122.7491
111.1627
111.1628
119.4368
119.4297
109.1074
100.14
101.162
103.311
118.3785
120.4498
119.4464
105.572
122.7780
121.5778
122.6917
116.3032
121.6205
118.3884
120.4700
115.2456
111.1595
111.1597
121.6192
121.5526
97.8646
112.1856
118.3572
1227
1240
1246
1248
1254
1255
1256
1261
1262
1263
1265
1267
1274
1275
1278
1279
1280
1288
1289
1292
1294
1295
1298
1302
1308
1310
1311
1312
1316
1336
1342
1475
1480
1481
1485
1489
1494
1495
1496
1505
1520
1536
1541
1542
232.1183
232.5030
232.3164
232.938
232.2005
232.3779
232.2602
232.4445
232.2416
232.2415
232.638
232.4135
232.4848
232.4850
232.4042
232.4043
232.4370
232.2278
232.2277
232.3394
232.1368
232.2024
232.677
232.3437
232.3177
232.3254
232.2116
232.4363
232.962
232.3186
232.712
232.1917
232.4800
232.1729
232.2135
232.3919
232.3475
232.768
232.769
232.3763
232.1052
232.3906
232.3211
232.3215
350.3932
362.6634
334.3374
345.3716
362.6328
342.3636
354.4146
360.4940
361.5589
355.4172
361.5857
311.2740
359.4700
359.4701
344.3711
353.4096
361.5651
357.4426
235.1397
362.6606
360.5148
300.2505
362.6560
360.4897
342.3651
319.2950
360.5174
202.1000
361.5797
307.2653
329.3216
361.5475
324.3086
359.4740
353.4121
258.1727
180.783
358.4517
261.1772
266.1852
147.506
245.1540
359.4743
361.5365
pheT
cobN
uvrC
coaD
dapF
leuS
pgi
purN
argC
ribA
petF2
htpG
rpl28
dxs
pykF
purK
aroB
nadA
trpS
thrB
folB
glgB
hemE
hisIE
dnaA
Phenylalanyl-tRNA synthetase beta subunit
cobalamin biosynthetic protein CobN
Excinuclease ABC subunit C (UvrC)
putative pantetheine-phosphate adenylyltransferas
diaminopimelate epimerase
leucyl-tRNA synthetase
glucose-6-phosphate isomerase
phosphoribosylglycinamide formyltransferase
N-acetyl-gamma-glutamyl-phosphate reductase
possible GTP cyclohydrolase II
probable methylthioadenosine phosphorylase
conserved hypothetical protein
Ferredoxin
Inositol monophosphatase family protein
heat shock protein HtpG
50S ribosomal protein L28
Alkyl hydroperoxide reductase
conserved hypothetical protein
conserved hypothetical protein
1-deoxy-D-xylulose 5-phosphate synthase
conserved hypothetical protein
conserved hypothetical membrane protein
pyruvate kinase
conserved hypothetical protein
phosphoribosylaminoimidazole carboxylase
3-dehydroquinate synthase
conserved hypothetical protein
conserved hypothetical protein
Quinolinate synthetase A protein
conserved hypothetical protein
putative endonuclease
t-RNA synthetase, class Ib:Tryptophanyl-tRNA sy
Putative glucokinase
putative homoserine kinase
possible dihydroneopterin aldolase
conserved hypothetical protein
1,4-alpha-glucan branching enzyme
Uroporphyrinogen decarboxylase (URO-D)
conserved hypothetical protein
histidine biosynthesis bifunctional protein HisIE
conserved hypothetical protein
chromosomal replication initiator protein DnaA
putative multidrug efflux ABC transporter
possible ATP phosphoribosyltransferase
Table 2
ort270
ort015
ort361
ort562
ort316
ort240
ort498
ort642
ort564
ort646
ort193
ort254
ort199
ort500
ort353
ort092
ort483
ort051
ort219
ort196
ort657
ort431
ort640
ort543
ort014
ort356
ort446
ort334
ort365
ort479
ort404
ort094
ort307
ort306
ort416
ort314
ort389
ort231
ort408
ort299
ort424
ort208
ort050
ort455
Pag
7.6650
4.8353
3.8031
6.4254
11.7503
4.1980
4.1614
5.1686
7.5409
7.1418
7.0170
7.8605
5.0733
4.8821
3.0155
10.8625
2.5462
4.4652
11.7647
3.6021
5.0849
3.4373
8.7114
4.5350
4.1781
8.7576
3.0337
5.8052
2.8153
5.8949
7.3519
5.3471
2.7912
2.3021
2.6303
9.2178
3.1462
7.5093
3.5785
2.8794
2.1290
1.8307
7.7359
5.8213
0
0
1
0
0
1
1
1
0
0
0
0
0
1
1
0
1
0
0
1
1
1
0
1
1
0
1
0
1
0
0
1
0
1
1
0
1
0
1
1
1
1
0
0
all0580
alr4907
all4936
all0082
all3722
all4751
all4845
alr4846
alr4848
alr1343
asr1344
alr3885
alr0912
alr1956
alr1952
all2707
alr2708
all1359
all0859
alr0577
alr4746
alr4745
alr0175
all0174
alr1080
alr1026
alr1312
all0980
alr3858
all1522
all4956
alr4957
all4358
all4357
all2315
alr2082
all1985
alr5252
alr2895
all4480
all2508
asr1309
alr3210
all1663
gll3339
gll3101
gll3141
gll1250
gll0378
gll3525
glr3128
gll0444
gll0217
gll0403
gsl0402
gll1462
glr4422
gll3611
gll2639
glr3481
glr1529
gll0551
glr1731
glr0841
gll2556
glr3029
gll0554
glr3125
glr0547
glr1074
glr4015
gll0297
gll0298
gll0762
gll3085
glr3086
gll3767
gll3766
gll2657
glr2448
glr1446
gll0127
gll4314
glr1809
glr2763
gsl2877
gll3950
gll3492
Online Supporting Information
0559
1263
1264
1265
1268
1269
1270
1271
1273
1274
1275
1278
1281
1284
1286
1287
1288
1291
1292
1293
1297
1298
1299
1300
1301
1302
1305
1306
1309
1310
1311
1312
1313
1314
1315
1316
1165
0431
0430
0428
0420
0418
0415
0413
1194
0379
0378
0375
0370
0368
0367
0366
0364
0363
0362
0358
0355
0351
0349
0348
0347
0344
0343
0341
0336
0335
0334
0332
0331
0330
0323
0322
0319
0318
0317
0316
0315
0314
0313
0312
0283
0276
0274
0272
0257
0254
0233
0230
497.164
475.90
391.13
415.14
490.103
505.119
427.15
427.33
427.36
507.192
507.193
432.28
506.199
420.3
497.173
493.84
493.68
458.2
424.30
497.24
505.106
505.105
407.13
407.15
498.138
498.56
497.129
415.32
502.61
505.93
477.85
477.33
463.67
463.68
375.2
388.7
507.46
475.52
431.41
441.50
464.47
464.31
495.2
416.11
133.1213
129.545
128.486
136.2416
135.2060
131.809
135.1880
135.1934
136.2261
134.1536
134.1537
134.1375
136.2644
135.1742
135.1738
135.2009
135.1825
133.1326
134.1371
131.881
124.107
124.106
124.105
121.9
126.240
126.241
131.850
131.851
131.854
131.856
131.868
131.857
129.594
129.595
133.1141
133.1193
125.210
134.1420
135.1890
135.1922
136.2267
136.2287
128.520
133.1169
0561
1337
1338
1339
1342
1343
1344
1345
1347
1348
1349
1352
1355
1358
1360
1361
1362
1365
1366
1367
1371
1372
1373
1374
1375
1376
1379
1380
1383
1384
1385
1386
1387
1388
1389
1390
1268
0427
0426
0424
0419
0417
0413
0412
sll1019
sll0902
sll1463
slr0066
sll0099
slr0400
sll0454
sll1108
slr1882
sll0635
ssr0102
sll1489
slr0321
slr2047
slr1531
sll0169
slr1934
sll0844
slr0819
slr1761
slr0546
slr1096
slr1673
slr0017
slr1022
sll1612
sll0996
slr1874
sll1633
slr0526
sll1917
slr1972
slr0164
slr0165
sll1363
slr1925
slr0638
sll1653
sll1893
slr0056
slr0604
ssl2667
slr2143
slr0528
tll1639
tll1106
tlr0528
tlr2152
tll0172
tll0858
tlr0690
tll1786
tll1556
tlr1947
tsl0811
tll1189
tlr0056
tll0037
tlr1973
tlr0758
tlr1169
tlr2256
tll1667
tlr1102
tll0698
tll0868
tll1968
tll0780
tlr1328
tlr0190
tlr1315
tll0523
tll2382
tlr0279
tll1192
tll0008
tll1759
tlr1071
tll2254
tlr2377
tll1034
tll2373
tlr1185
tll1539
tlr0304
tsl1293
tll2327
tlr1239
117.3507
112.1696
106.637
111.1559
107.823
95.8446
106.635
106.737
119.4305
122.6515
122.6516
122.7243
97.8579
93.8377
93.8373
97.8639
97.8597
118.3701
120.5101
103.326
95.8485
95.8483
95.8481
95.8458
122.6586
122.7876
116.2972
120.5122
117.3167
122.6229
114.2234
114.2240
121.5914
121.5915
117.3269
119.4179
120.4809
120.4913
111.1638
114.2264
98.8681
113.2079
121.6038
120.4586
1543
1586
1587
1590
1596
1599
1600
1601
1603
1604
1605
1608
1613
1616
1618
1619
1620
1622
1623
1625
1629
1630
1631
1633
1634
1635
1640
1641
1644
1645
1646
1647
1648
1649
1650
1651
1671
1674
1675
1677
1684
1687
1689
1690
232.4218
232.1162
232.1196
232.5308
232.2457
232.895
232.1086
232.1087
232.1089
232.3884
232.3883
232.787
232.3381
232.3223
232.3226
232.3144
232.3145
232.2942
232.3328
232.4221
232.900
232.901
232.5289
232.5288
232.2623
232.2579
232.1955
232.4248
232.815
232.2794
232.1185
232.1184
232.5162
232.5161
232.4034
232.2041
232.3205
232.5275
232.4874
232.2245
232.4326
232.1952
232.3718
232.5010
357.4363
357.4406
251.1628
233.1372
258.1729
69.89
305.2609
300.2497
362.6378
346.3783
346.3784
284.2156
321.3013
357.4455
261.1775
226.1278
226.1283
351.4024
354.4153
282.2138
362.6707
300.2494
185.829
185.821
360.5161
355.4176
351.3979
357.4357
356.4290
318.2924
361.5610
361.5635
360.4873
360.4874
359.4730
279.2057
262.1794
359.4679
253.1658
362.6019
157.582
360.5037
316.2875
346.3769
argF
ftsH3
ribD
cobL
pheS
surE
ribF
thiE
phoH
ffh
pdhA
trpC
lpdA
spoU
murA
argD
folC
miaB
ddlB
ftsZ
panB
hemN
clpP4
clpP3
ilvC
cobD
glyQ
hisF
chlG
lepA
murE
Putative hydroxyacylglutathione hydrolase
ornithine carbamoyltransferase
cell division protein FtsH3
riboflavin biosynthesis protein
putative precorrin-6y methylase
predicted sugar kinase
Phenylalanyl-tRNA synthetase:Aminoacyl tRNA s
Survival protein SurE
putative riboflavin kinase/FAD synthase
Thiamine monophosphate synthase (TMP)
DUF170
putative circadian phase modifier CpmA homolog
GTP-binding protein ERA homolog
PhoH-like phosphate starvation-inducible protein
signal recognition particle protein (SRP54)
conserved hypothetical protein
Pyruvate dehydrogenase E1 alpha subunit
tRNA (5-methylaminomethyl-2-thiouridylate)-methyl
possible apolipoprotein n-acyltransferase
FKBP-type peptidyl-prolyl cis-trans isomerase (PP
Indole-3-glycerol phosphate synthase:Proteins bin
putative dihydrolipoamide dehydrogenase
tRNA/rRNA methyltransferase (SpoU)
UDP-N-glucosamine 1-carboxyvinyltransferase
putative N-acetylornithine aminotransferase
putuative bifunctional Dihydrofolate/Folylpolyglutam
2-methylthioadenine synthetase
D-alanine--D-alanine ligase
cell division protein FtsZ
putative Ketopantoate hydroxymethyltransferase
possible oxygen independent coproporphyrinogen III
conserved hypothetical protein
ATP-dependent Clp protease proteolytic subunit 4
ATP-dependent Clp protease proteolytic subunit 3
ketol-acid reductoisomerase
putative cobalamin biosynthetic protein
glycyl-tRNA synthetase alpha subunit
possible menaquinone biosynthesis methyltransferase
Imidazole glycerol phosphate synthase subunit His
chlorophyll synthase 33 kD subunit
GTP-binding protein LepA
NifU-like protein
putative L-cysteine/cystine lyase
UDP-N-acetylmuramyl-tripeptide synthetase
Table 2
Pag
ort095
ort621
ort228
ort312
ort096
4.0832
2.7493
8.3158
5.5048
8.7226
1
0
0
0
0
asr1611
alr2737
all3075
alr2377
asr2378
gsl1913
gll3572
glr2715
glr1772
gsr1647
0411
0410
1159
1160
1161
0228
0227
1181
1183
1184
483.85
468.69
493.24
506.211
506.212
133.1167
133.1312
136.2413
136.2673
135.1904
0410
0409
1257
1259
1260
ssl0331
slr0469
sll0905
slr0618
ssr1041
tsr0564
tlr0147
tlr1302
tll1716
tsl1557
122.6916
116.2921
121.6055
120.4741
120.4743
1693
1694
1702
1704
1705
232.3092
232.3172
232.4708
232.4094
232.4095
357.4321
203.1009
289.2247
284.2173
284.2174
ort555
7.9203
0
alr1526
glr2158
0551
1204
454.3
133.1285
0552
slr0012
tll1504
117.3212
1717
232.2790
310.2716
ort553
ort097
ort303
ort297
ort302
1.8375
4.1880
8.4178
8.7604
4.5780
1
1
0
0
0
alr1524
all3257
all5076
alr3441
all5078
glr2156
glr1519
gll2369
glr0215
gll2370
0550
0547
0545
0544
0543
1205
1208
1215
1216
1217
454.1
464.26
431.26
498.157
431.23
133.1284
136.2832
133.1278
135.2069
133.1277
0551
0548
0546
0545
0544
slr0009
slr0169
slr0750
slr0772
slr0749
tll1506
tlr0311
tll2345
tll2392
tll2347
117.3210
113.1896
122.6336
117.3130
122.6334
1718
1721
1723
1724
1725
232.2792
232.3757
232.1291
232.2368
232.1293
310.2714
195.926
351.4018
199.967
351.4016
ort481
ort060
ort659
ort001
ort098
ort099
ort100
ort415
ort401
ort319
ort624
ort643
ort362
ort230
ort313
ort258
ort505
ort515
ort532
ort012
ort511
ort636
ort399
ort052
ort101
ort102
ort194
ort403
ort103
ort104
ort441
4.3930
7.1721
7.9147
3.4536
3.9756
3.6335
9.4567
3.4278
3.7613
4.3761
4.2273
3.8232
7.5192
11.9224
5.8107
9.0805
3.6335
5.5852
2.8405
3.6693
6.2271
2.8669
3.9627
9.8892
3.3443
7.6973
6.4252
1.9856
3.3323
5.8508
3.0569
1
0
0
1
1
1
0
1
1
1
1
1
0
0
0
0
1
0
1
1
0
1
1
0
1
0
0
1
1
0
1
all1743
alr1961
all5288
alr5285
alr5284
alr5283
all5255
all4613
alr3751
all3802
alr1208
all2563
alr0718
all3785
alr3338
alr3339
all3570
alr5053
alr4784
alr1245
all4248
all5263
alr1878
asr4549
alr1093
all0200
all5306
alr3265
all4664
all4665
all1019
glr2486
glr3295
gll0754
gll2864
gll3145
gll3146
gll3765
glr3279
gll0839
glr0385
glr0288
gll1597
glr2929
gll3175
gll0771
gll3822
glr4227
gll2525
glr3280
gll3931
gll0025
glr2572
glr3212
gsl1645
glr3817
gll0542
glr0140
glr0071
gll2901
glr0255
glr0412
0542
0539
0537
0534
0533
0532
0528
0526
0525
0523
0521
0519
0518
0516
0515
0514
0511
0508
0506
0499
0497
0496
0495
0491
0490
0487
0484
0483
0480
0479
0477
1218
1224
1226
1229
1230
1231
1235
1239
1240
1243
1245
1248
1249
1251
1252
1253
1257
1259
1261
1268
1271
1272
1273
1283
1284
1291
1294
1296
1301
1302
1305
474.17
483.31
468.14
468.73
468.72
468.71
455.47
468.52
397.2
505.29
450.14
424.11
459.5
506.47
489.101
489.102
508.104
418.28
487.84
506.18
509.85
483.42
402.15
373.14
452.27
472.89
474.61
505.173
464.2
435.48
498.108
129.613
133.1209
136.2785
135.1627
135.1626
135.1625
136.2749
136.2635
136.2632
126.245
136.2827
131.907
136.2266
136.2264
136.2818
136.2819
133.1224
135.1834
125.177
133.1164
127.380
127.325
126.250
135.2158
126.244
131.839
136.2536
127.376
132.1041
132.1040
125.149
0543
0540
0538
0534
0533
0532
0528
0526
0525
0523
0521
0519
0518
0516
0515
0514
0510
0508
0506
0499
0497
0495
0494
0490
0489
0486
0483
0482
0478
0477
0475
slr0506
sll0809
sll0356
sll0728
sll0209
sll0208
slr1573
slr2088
slr0839
slr0260
sll0145
slr1793
sll1833
slr0959
slr1124
sll1018
slr1622
sll1425
sll1823
slr1898
sll0270
slr0653
slr1887
ssl2296
slr0609
slr1411
sll1854
sll0017
slr1926
slr0039
sll0555
tlr0575
tlr0228
tll2272
tll1311
tll1312
tll1313
tll2307
tlr1296
tlr2216
tlr0265
tll0259
tll0467
tlr2074
tlr1890
tlr1532
tlr1533
tll1883
tlr0777
tll0531
tll1408
tll0415
tll0617
tll1646
tsl1825
tlr2276
tll2296
tlr1785
tlr0479
tlr0863
tlr2026
tll0424
122.7943
122.7442
120.4765
119.4335
122.6742
122.6741
113.2045
121.5292
117.3282
116.2714
117.3155
121.5841
115.2584
109.1219
109.1081
109.1083
122.7810
112.1826
121.5788
101.151
104.436
97.8595
122.6982
91.8284
122.7669
118.3643
94.8387
121.5195
121.6188
121.6187
121.5861
1726
1731
1733
1736
1737
1738
1742
1746
1747
1750
1753
1759
1760
1762
1763
1764
1769
1771
1773
1780
1782
1783
1785
1794
1795
1802
1807
1809
1818
1819
1822
232.4185
232.3219
232.1491
232.1488
232.1487
232.1486
232.5272
232.1693
232.5423
232.873
232.4506
232.4377
232.3478
232.5395
232.2549
232.2548
232.2448
232.1272
232.1024
232.4435
232.5055
232.5263
232.3629
232.1464
232.2611
232.1631
232.1511
232.3765
232.970
232.969
232.2573
318.2919
358.4539
359.4710
235.1404
334.3385
361.5731
184.818
361.5428
291.2281
289.2248
113.282
346.3782
203.1021
335.3409
335.3401
326.3134
288.2235
357.4342
357.4351
362.6710
321.3016
361.5683
295.2369
362.6672
361.5580
362.6650
262.1783
307.2647
162.628
361.5799
358.4501
Online Supporting Information
rpsD
cobB
cbbS,
rbcS
cbbL,
rbcL
chlN
chlB
chlL
pcr,
por
trpF
accA
ilvB
hemH
cobO
rrf
tal
ftsI
cobC
ppa
proS
purA
argB
priA
sigA
hemC
hemL
map
conserved hypothetical protein
30S ribosomal protein S4
possible Maf-like protein implicated in septum forma
Cobyric acid synthase CobB
conserved hypothetical protein
Ribulose bisphosphate carboxylase, small chain
Ribulose bisphosphate carboxylase, large chain
conserved hypothetical protein
possible light-independent protochlorophyllide reduct
light-independent protochlorophyllide reductase ChlB
Protochlorophyllide reductase iron-sulfur
Light dependent protochlorophyllide oxido-reduct
Biotin/lipoate A/B protein ligase family
phosphoribosylanthranilate isomerase
acetyl-CoA carboxylase, alpha subunit
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
acetolactate synthase
Ferrochelatase
possible cob(I)alamin adenosyltransferase
ribosome recycling factor protein Rrf
transaldolase
putative peptidoglycan synthetase (pbp transpeptidase
Possible membrane associated protease
putative alpha-ribazole-5'-P phosphatase
putative dihydroorotase
inorganic pyrophosphatase
Prolyl-tRNA synthetase
Adenylosuccinate synthetase
acetylglutamate kinase
primosomal protein N' (replication factor Y)
Putative principal RNA polymerase sigma factor
Porphobilinogen deaminase
4a-hydroxytetrahydrobiopterin dehydratase (PCD)
conserved hypothetical protein
conserved hypothetical protein
exodeoxyribonuclease III
glutamate-1-semialdehyde 2,1-aminomutase
conserved hypothetical protein
conserved hypothetical protein
putative methionine aminopeptidase
Table 2
ort583
ort387
ort289
ort250
ort488
ort486
ort680
ort317
ort508
ort670
ort421
ort350
ort277
ort275
ort325
ort105
ort563
ort279
ort106
ort653
ort467
ort040
ort668
ort107
ort271
ort108
ort635
ort610
ort503
ort284
ort198
ort459
ort023
ort520
ort360
ort489
ort487
ort447
ort448
ort449
ort109
ort402
ort521
ort615
Pag
2.4088
5.2403
8.4611
4.4184
3.0326
3.9123
5.2465
5.2407
5.6955
8.3222
7.0685
3.6287
4.6512
4.8385
8.3212
9.5613
6.6652
7.2745
8.5202
4.6648
3.4549
10.9163
6.4108
4.4849
4.0526
4.9635
4.2058
2.4249
3.1232
5.9013
4.5751
6.6462
5.8973
3.2338
5.8556
1.7277
1.1236
######
3.9291
4.1129
9.1011
9.2934
2.1642
1.6101
1
0
0
1
0
0
0
0
0
0
0
1
1
0
0
0
1
0
0
0
1
0
0
0
0
0
1
1
1
0
1
0
0
1
0
1
1
0
1
1
0
0
1
1
alr5297
all3205
all4374
all2456
all2453
all2452
all4699
all4698
all3552
alr3553
all5167
alr1894
alr2373
alr2372
all0948
all0949
all5258
alr5260
alr0297
alr2780
all4883
alr5256
all4012
alr3414
alr3415
all4296
all3976
all3969
all4396
all4680
alr3739
all0049
alr2782
asr4319
alr4320
alr3422
alr3421
alr3455
alr3456
asr3457
alr0116
alr0115
all0138
all0136
glr0828
gll2378
glr1622
gll1912
glr3038
glr3039
gll4393
gll1377
gll0510
glr3428
glr2791
glr3506
glr2168
glr2167
glr2166
glr2165
glr3604
gll3752
glr4139
glr3198
glr3120
gll1338
glr2705
glr1476
glr2231
glr1649
glr0716
gsl3914
gll3149
gll3021
glr4375
glr3637
glr2442
gsl3408
gll3407
gll1918
gll1919
glr1992
glr1993
gsr1994
glr3274
glr1755
glr2999
glr0987
Online Supporting Information
0475
0473
0466
0464
0462
0461
0460
0459
0457
0456
0454
0453
0450
0449
0448
0447
0442
0441
0439
0436
0435
0433
1181
1185
1186
1187
1188
1190
1191
1193
0218
0217
0387
0329
0328
0326
0325
0322
0321
0320
0319
0318
0315
0312
1306
1308
1319
1320
1322
1323
1324
1325
1327
1328
1330
1333
1337
1338
1339
1340
1346
1348
1350
1353
1354
1359
1366
1370
1371
1373
1374
1376
1377
1379
1544
1546
0195
0187
0186
1648
1649
1652
1653
1654
1659
1660
1665
1668
354.22
345.1
482.129
506.80
506.86
506.87
452.58
452.59
482.64
482.59
498.69
362.19
506.208
506.206
493.120
493.119
455.45
455.15
484.95
482.133
456.29
455.12
412.23
507.95
507.96
507.100
357.10
357.13
375.11
422.12
398.35
506.160
373.1
452.35
452.37
509.270
509.269
504.122
504.123
504.124
370.3
370.2
494.8
494.9
129.556
131.864
134.1450
135.2188
124.82
124.83
124.84
124.85
135.1837
135.1999
127.311
127.402
130.661
130.660
136.2540
136.2539
135.2166
134.1436
131.927
133.1274
133.1206
136.2348
135.2022
135.1642
135.1643
135.1646
136.2288
136.2291
125.155
136.2657
126.261
127.354
126.288
128.451
128.452
131.827
131.826
135.1975
126.213
126.214
135.1790
135.1789
127.302
127.306
0473
0471
0464
0462
0460
0459
0458
0457
0456
0455
0453
0452
0446
0445
0444
0443
0438
0437
0435
0432
0431
0429
1297
1301
1302
1303
1304
1306
1307
1309
0246
0245
0384
0371
0370
0368
0367
0364
0363
0362
0360
0359
0354
0351
sll1740
sll0179
slr0880
sll0194
sll1316
sll1317
sll1187
slr0239
sll1546
slr0926
slr0951
slr0886
sll0760
sll0759
sll1899
sll1898
sll0300
slr1520
sll1500
slr2058
sll0223
sll1655
sll0109
slr1470
slr1471
slr0480
slr1703
slr0628
sll1043
sll0818
slr1090
sll1772
sll1112
ssr2831
slr1689
slr0343
slr0342
sll0288
sll0289
ssl0546
sll1866
sll1237
slr0906
slr1356
tlr1303
tll0506
tll2058
tlr0953
tlr0959
tlr0960
tll2157
tlr0563
tll1680
tlr0402
tlr0605
tlr1502
tll1324
tlr0010
tll1893
tll1894
tlr1686
tlr2042
tll2306
tll1881
tll0045
tll1111
tll1803
tll0601
tll0600
tll0076
tlr1552
tll1826
tll2193
tlr1514
tll2353
tlr2472
tlr0494
tsl1567
tll1566
tlr0797
tlr0796
tlr2016
tlr2017
tlr2018
tll2123
tlr1836
tlr1530
tll2046
121.5555
121.5357
121.5283
115.2553
115.2492
115.2493
122.6320
122.6321
113.1977
113.1993
118.3942
121.6008
108.944
120.5080
115.2523
115.2522
122.6503
122.7629
122.6319
122.7660
93.8370
113.1937
105.523
122.7227
122.7228
122.7231
106.673
121.5779
122.6329
122.7874
120.5042
121.5587
122.6607
121.6202
121.6203
101.117
101.116
113.2066
113.2067
113.2068
116.2865
116.2862
122.6941
122.6943
1824
1826
1838
1839
1841
1842
1843
1844
1846
1847
1849
1852
1857
1858
1859
1860
1865
1867
1869
1872
1873
1876
1885
1889
1890
1892
1894
1896
1897
1899
1928
1931
1938
1960
1961
1966
1967
1970
1971
1972
1975
1976
1982
1985
232.1502
232.3713
232.2209
232.4275
232.4273
232.4272
232.939
232.940
232.2430
232.2431
232.1369
232.2657
232.4090
232.4089
232.4409
232.4410
232.5269
232.5267
232.1981
232.3932
232.1122
232.5271
232.673
232.2337
232.2338
232.5105
232.705
232.713
232.2185
232.959
232.5435
232.1592
232.3934
232.5127
232.5128
232.2345
232.2344
232.2379
232.2380
232.2381
232.5335
232.5334
232.5357
232.5355
289.2249
361.5986
360.4952
357.4361
201.991
319.2936
360.5189
327.3183
272.1948
361.5393
289.2244
292.2303
362.6704
362.6673
362.6661
362.6660
306.2643
306.2627
360.5199
358.4636
362.6309
361.5316
268.1885
359.4795
359.4796
252.1632
257.1711
263.1798
358.4563
204.1029
171.702
331.3287
361.5527
118.312
118.313
356.4240
356.4239
155.566
155.567
155.568
247.1572
358.4534
77.123
335.3414
rpl19
gltX
petC
petA
yvoC
cobM
ppx
ubiA
ispD
fabG
ctaB
ribE
topA
ndhB
birA
tyrA
serRS
rps14
pnp
mutS
aroD
psaE
fpg
petD
petB
minC
minD
minE
hemK
psbB
rps1a
possible 50S ribosomal protein L19
glutamyl-tRNA synthetase
similar to secreted protein MPB70 precursor
protein secretion component, Tat family
Cytochrome b6f complex subunit (Rieske iron-sulfur p
apocytochrome f
putative prolipoprotein diacylglyceryl transferase
PUTATIVE PRECORRIN-4 C11-METHYLTRANSF
putative exopolyphosphatase
probable 4-hydroxybenzoate-octaprenyltransferase
putative 2-C-methyl-D-erythritol 4-phosphate cytidyl
3-oxoacyl-[acyl-carrier protein] reductase
putative multidrug efflux ABC transporter
putative multidrug efflux ABC transporter
putative protoheme IX farnesyltransferase
conserved hypothetical protein
Putative Riboflavin synthase alpha chain
putative oxidoreductase, aldo/keto reductase family
conserved hypothetical protein
Prokaryotic DNA topoisomerase
NADH dehydrogenase I chain 2 (or N)
putative Biotin--acetyl-CoA-carboxylase ligase
Chorismate mutase
conserved hypothetical protein
Putative inner membrane protein
conserved hypothetical protein
putative seryl-tRNA synthetase
30S ribosomal protein S14
polyribonucleotide nucleotidyltransferase
putative tetrapyrrole methylase family protein
GTP1/Obg family GTP-binding protein
putative DNA mismatch repair protein MutS family
Dehydroquinase class II
photosystem I subunit IV (PsaE)
Formamidopyrimidine-DNA glycolase (FAPY-DNA g
cytochrome b6f complex subunit 4 (17 kd polypeptid
apocytochrome b6
possible septum site-determining protein
putative septum site-determining protein MinD
possible septum site-determining protein MinE
conserved hypothetical protein
possible protoporphyrinogen oxidase
photosystem II chlorophyll-binding protein CP47
30S ribosomal protein S1, homolog A
Table 2
ort444
ort252
ort274
ort480
ort540
ort568
ort110
ort206
ort111
ort519
ort658
ort112
ort506
ort557
ort113
ort450
ort114
ort212
ort241
ort115
ort116
ort556
ort117
ort272
ort118
ort593
ort597
ort588
ort584
ort614
ort587
ort617
ort580
ort592
ort612
ort601
ort589
ort598
ort620
ort599
ort582
ort622
ort579
ort633
Pag
2.6998
7.5240
6.7345
6.4817
11.4171
5.2948
9.6354
4.7836
8.9527
4.1518
4.6495
6.3363
4.1691
6.4191
5.9256
2.7706
7.4787
6.2936
9.1785
9.9210
7.5851
1.8121
11.0019
7.5610
5.7911
3.4338
4.2138
4.8482
2.8292
1.6236
2.7470
2.3864
1.7309
5.4025
3.2755
2.2454
3.6335
2.0908
3.2022
4.2082
4.0830
2.3137
4.0651
3.3749
1
0
0
0
0
0
0
1
0
1
0
0
1
0
0
1
0
0
0
0
0
1
0
0
0
1
1
1
1
1
1
1
1
0
1
1
1
1
1
1
1
1
1
1
alr4124
all4656
alr5068
alr2936
alr3525
all3791
alr3980
alr0652
alr2572
all0329
all0328
alr3351
all4861
all3374
alr1286
all2906
alr5126
all5123
all1141
alr4075
asr4076
all3272
alr3863
alr2308
alr4216
all4215
all4214
all4213
all4212
asl4211
all4210
all4209
all4208
asl4207
asl4206
all4205
asl4204
all4203
all4202
all4201
all4200
all4199
all4198
all4197
gll2577
gll0781
gll3174
gll1806
gll0720
gll3123
glr3763
glr1480
glr1586
glr3701
glr1717
glr2275
gll0414
gll2405
gll2047
gll3412
gll3173
gll2874
glr0406
glr1449
gsl3135
gll3416
glr2043
gll3769
gll3770
glr0085
glr0086
glr0087
glr0903
gsr0904
gll3922
gll3921
gll3920
gsl3919
gsl3918
gll3917
gll3916
gll3915
gll3913
gll3912
gll3911
gll3910
gll3909
gll1393
Online Supporting Information
0311
0310
1591
1590
1589
1584
1583
1581
1579
1578
1577
1576
1575
1573
1571
1569
1567
1566
1565
1564
1563
1562
1561
1560
1559
1558
1557
1556
1555
1554
1553
1552
1551
1550
1549
1548
1547
1546
1545
1544
1543
1542
1541
1540
1670
1671
1688
1689
1691
1703
1704
1707
1709
1710
1711
1712
1713
1715
1717
1719
1722
1723
1724
1725
1726
1727
1728
1730
1731
1732
1733
1734
1735
1736
1737
1738
1739
1740
1741
1742
1743
1744
1745
1746
1747
1748
1749
1750
474.106
464.9
418.37
461.69
461.72
505.114
357.7
302.2
421.30
485.8
485.9
346.3
458.16
450.37
456.38
391.20
386.17
406.9
389.1
507.14
507.16
324.3
372.20
481.68
374.3
374.12
374.13
374.14
374.15
374.16
374.17
374.18
374.19
374.20
374.21
374.22
374.23
374.24
374.25
374.27
374.28
374.29
374.30
374.31
129.637
129.638
136.2278
134.1385
132.1028
127.397
127.313
134.1416
133.1150
134.1500
134.1501
131.939
131.940
131.942
133.1260
136.2440
135.1986
126.252
127.383
127.317
127.318
136.2347
127.367
127.363
130.685
130.702
130.703
130.704
130.705
130.706
130.707
130.708
130.709
130.710
130.711
130.712
130.713
130.714
130.715
130.716
130.717
130.718
130.719
130.720
0349
0348
1747
1746
1745
1740
1739
1736
1734
1733
1732
1731
1730
1728
1726
1724
1721
1720
1719
1718
1717
1716
1715
1714
1713
1712
1711
1710
1709
1708
1707
1706
1705
1704
1703
1702
1701
1700
1699
1698
1697
1696
1695
1694
sll0927
slr1420
slr0328
sll1249
slr0838
sll0320
slr0589
slr0067
slr1285
slr0737
slr0738
slr0990
sll0920
sll1277
slr1717
sll1536
slr1563
slr1293
slr2081
slr1495
ssr0332
sll0569
sll0295
sll0031
sll1262
sll1799
sll1800
sll1801
sll1802
ssl3432
sll1803
sll1804
sll1805
ssl3436
ssl3437
sll1806
sll1807
sll1808
sll1809
sll1810
sll1811
sll1812
sll1813
sll1814
tll0978
tll1291
tlr1810
tll2450
tlr1811
tlr1083
tll0625
tlr2419
tlr1565
tll1724
tll1672
tll0322
tll1912
tll2444
tll1241
tlr2403
tlr1821
tll0232
tll2435
tlr1240
tsl2097
tlr2089
tlr1691
tlr0739
tlr1130
tlr0081
tlr0082
tlr0083
tlr0084
tsr0085
tlr0086
tlr0087
tlr0088
tsr0089
tsr0090
tlr0091
tlr0092
tlr0093
tlr0094
tlr0095
tlr0096
tlr0097
tlr0098
tlr0099
122.6945
119.4142
120.4679
121.6145
121.5252
116.2883
120.4770
101.90
119.4342
117.3514
117.3515
121.5582
116.3099
111.1601
122.7215
108.980
99.8746
117.3387
122.6634
122.7496
122.7498
122.6631
122.6543
99.8758
99.8757
99.8766
99.8767
99.8768
99.8769
99.8770
99.8771
99.8772
99.8773
99.8774
99.8775
99.8776
99.8777
99.8778
99.8779
99.8780
99.8781
99.8782
99.8783
99.8784
1987
1988
2026
2027
2029
2036
2038
2041
2043
2044
2045
2046
2047
2049
2051
2053
2056
2057
2058
2059
2060
2062
2063
2065
2066
2067
2068
2069
2070
2071
2072
2073
2074
2075
2076
2077
2078
2079
2080
2081
2082
2083
2084
2085
232.4655
232.977
232.1284
232.4831
232.2123
232.889
232.702
232.3443
232.4385
232.3578
232.3577
232.2104
232.1104
232.2294
232.1930
232.4861
232.1299
232.1302
232.3264
232.2057
232.2056
232.3769
232.811
232.4026
232.4566
232.4567
232.4568
232.4569
232.4570
232.4571
232.4572
232.4573
232.4574
232.4575
232.4576
232.4577
232.4578
232.4579
232.4580
232.4581
232.4582
232.4583
232.4584
232.4585
361.5852
255.1690
231.1345
362.6150
312.2767
360.5036
321.3009
205.1043
358.4523
344.3693
344.3694
315.2858
297.2431
269.1897
326.3155
151.536
332.3320
362.6111
357.4419
225.1269
361.5834
76.118
360.5108
339.3546
362.6376
298.2439
298.2440
298.2441
298.2442
298.2443
298.2444
298.2445
298.2446
298.2447
298.2448
298.2449
296.2389
296.2390
296.2391
296.2392
296.2393
296.2394
296.2395
296.2396
metK
panC
purM
rnd
psaD
trpE
ppc
recF
moeB
recA
rpl3
rpl4
rpl23
rpl2
rps19
rpl22
rps3
rpl16
rpl29
rps17
rplN
rpl24
rpl5
rps8
rpl6
rpl18
rpsE
rpl15
secY
S-adenosylmethionine synthetase
Putative carbohydrate kinase, FGGY family
putative low molecular weight protein-tyrosine-phosp
putative bifunctional enzyme; pantothenate synthetase
phosphoribosyl formylglycinamidine cyclo-ligase
putative ribonuclease D
conserved hypothetical protein
MRP protein homolog
conserved hypothetical protein
photosystem I reaction center subunit II (PsaD)
Anthranilate synthase component I and chorismate bin
conserved hypothetical protein
phosphoenolpyruvate carboxylase
putative DNA repair and genetic recombination prote
conserved hypothetical protein
molybdopterin biosynthesis protein
conserved hypothetical protein
phytoene dehydrogenase related enzyme
Prephenate dehydrogenase
conserved hypothetical protein
conserved hypothetical protein
RecA bacterial DNA recombination protein
conserved hypothetical protein
putative ldpA protein
conserved hypothetical protein
50S ribosomal protein L3
50S ribosomal protein L4
50S ribosomal protein L23
50S ribosomal protein L2
30S ribosomal protein S19
50S ribosomal protein L22
30S ribosomal protein S3
50S ribosomal protein L16
50S ribosomal protein L29
30S ribosomal protein S17
50S ribosomal protein L14
50S ribosomal protein L24
50S ribosomal protein L5
30S ribosomal protein S8
50S ribosomal protein L6
50S ribosomal protein L18
30S ribosomal protein S5
50S ribosomal protein L15
preprotein translocase SecY subunit
Table 2
ort007
ort609
ort607
ort602
ort581
ort661
ort578
ort202
ort011
ort517
ort516
ort047
ort429
ort385
ort608
ort619
ort368
ort665
ort606
ort059
ort497
ort570
ort569
ort119
ort328
ort278
ort237
ort281
ort222
ort120
ort462
ort121
ort223
ort122
ort123
ort025
ort236
ort125
ort126
ort127
ort128
ort571
ort412
ort291
Pag
6.9091
2.3989
1.2622
3.7192
2.1533
6.1436
2.9475
2.8099
6.0994
1.3910
2.2075
9.9441
3.3616
3.8422
0.9678
2.8512
1.9792
1.7116
0.8543
4.7356
6.1800
7.7365
3.1798
3.9344
9.5744
7.9381
7.8222
7.6511
5.1723
9.7074
6.8213
8.4493
3.5794
6.3493
5.8153
6.5786
5.3009
5.2226
4.0985
7.1284
4.8971
2.0237
6.2940
9.3496
0
1
1
1
1
0
1
1
0
1
1
0
1
1
1
1
1
1
1
1
1
0
1
0
0
0
0
1
0
0
0
0
1
0
0
0
0
0
1
0
1
1
0
0
all4196
all4193
all4192
all4191
all4190
all4189
all4188
all2457
alr2458
alr5155
alr5154
all0453
all1694
alr4344
all4340
all4339
all4338
all4337
all4336
all4335
alr4334
alr4332
alr4331
asl4325
all4464
alr4094
all1802
all1800
all1211
alr1215
alr1217
all1220
alr1222
all4101
all4102
alr1244
alr0063
all2381
alr2385
alr2386
asr4321
all0129
all4705
all4708
gll1392
gll3574
gll3573
gll3571
gll3570
gll3569
glr4418
glr3730
glr3818
glr3439
glr3438
gll2546
gll1029
glr1508
glr3925
glr3926
glr3927
glr3928
glr3929
glr3968
gll0524
glr1507
glr1506
gsl0746
glr1656
glr3503
glr0515
glr0516
glr2775
glr3755
glr0846
glr2112
gll4317
gll0853
gll4038
glr2710
glr4032
gll0842
gll4382
glr3390
gsl3544
gll4162
gll1432
glr0678
Online Supporting Information
1539
1537
1536
1535
1534
1533
1532
1528
1527
1523
1524
1525
1514
1512
1511
1510
1509
1508
1507
1506
1504
1502
1501
1499
0081
0082
0084
0085
0098
0099
0100
0101
0102
0103
0104
0107
0112
0114
0116
0117
0121
0128
0129
0130
1751
1753
1754
1755
1756
1757
1758
1762
1763
1769
1770
1772
1775
1777
1779
1780
1781
1782
1783
1784
1786
1788
1789
1792
1624
1625
1628
1629
0181
0179
0177
0176
0175
0172
0170
0163
1963
1967
1969
1970
1975
1988
1989
1990
374.32
374.35
374.36
374.37
374.38
374.39
374.40
401.28
401.6
456.8
456.7
502.74
463.15
423.41
423.16
423.17
423.18
423.19
423.20
423.21
423.36
423.35
423.34
443.38
493.74
507.59
489.87
489.88
475.2
441.1
441.4
441.58
441.8
486.93
486.92
506.16
472.17
506.63
506.215
506.216
452.38
504.130
428.12
399.9
130.721
130.723
130.724
130.725
130.726
130.727
130.728
130.684
130.732
135.1944
135.1943
135.1783
136.2846
132.1054
132.1058
132.1060
132.1061
132.1062
132.1063
132.1064
132.1053
132.1052
132.1051
127.309
129.611
129.541
134.1554
134.1555
135.1840
133.1240
135.2046
135.1918
129.608
124.116
124.115
126.297
136.2342
133.1153
126.222
126.223
129.534
136.2478
136.2613
136.2612
1693
1691
1690
1689
1688
1687
1686
1682
1681
1673
1672
1671
1670
1668
1667
1666
1665
1664
1663
1662
1660
1658
1657
1654
0095
0096
0098
0099
0117
0118
0119
0120
0121
0123
0125
0128
0132
0135
0137
0138
0141
0150
0151
0152
sll1815
sll1816
sll1817
sll1818
sll1819
sll1820
sll1821
sll1193
slr0827
slr1835
slr1834
slr0969
slr1598
sll1499
sll1096
sll1097
sll1098
sll1099
sll1101
sll0195
sll1662
slr1130
slr1129
ssr2723
slr1791
slr1743
slr1509
sll0493
slr2030
slr1990
sll0631
slr0565
slr0082
slr0651
slr0656
sll1669
sll0754
slr0941
slr1417
sll1979
ssl1690
slr0115
slr0446
slr0379
tlr0100
tlr0103
tlr0104
tlr0105
tlr0106
tlr0107
tlr0108
tlr0496
tll0460
tlr0732
tlr0731
tll1307
tlr0613
tll1368
tlr1747
tlr1748
tlr1749
tlr1750
tlr1751
tlr2461
tlr2106
tll0663
tlr0597
tll0211
tll1035
tlr1136
tll0303
tlr0412
tll1647
tll0200
tll2408
tlr0588
tlr1564
tlr0351
tll1862
tlr0882
tll1629
tll0336
tll0867
tsl0866
tsl0017
tlr2423
tll0518
tlr2055
99.8785
99.8789
99.8790
99.8791
99.8792
99.8793
99.8794
122.6287
122.7861
122.6939
122.6938
117.3403
110.1280
122.6439
122.7700
122.7701
122.7702
122.7703
122.7704
122.7705
122.7706
122.6427
122.6426
98.8736
121.5284
119.4435
120.4792
120.4794
121.5510
120.4512
105.589
75.7991
121.5424
122.7777
122.7036
122.6361
104.471
120.4901
120.4747
120.4748
121.6204
122.6827
122.7849
122.7848
2086
2088
2089
2090
2091
2092
2093
2097
2098
2123
2124
2126
2130
2132
2135
2136
2137
2138
2139
2140
2142
2144
2145
2148
2164
2165
2168
2169
2188
2190
2192
2193
2194
2197
2198
2202
2207
2212
2214
2215
2219
2236
2237
2238
232.4586
232.4589
232.4590
232.4591
232.4592
232.4593
232.4594
232.4276
232.4277
232.1362
232.1361
232.1795
232.5025
232.5151
232.5147
232.5146
232.5145
232.5144
232.5143
232.5142
232.5141
232.5139
232.5138
232.5132
232.2234
232.4685
232.3659
232.3658
232.4509
232.4511
232.4513
232.4516
232.4518
232.4680
232.4679
232.4434
232.1604
232.4097
232.4100
232.4101
232.5129
232.5348
232.935
232.934
296.2397
296.2399
296.2400
296.2401
296.2402
296.2403
296.2404
360.5171
357.4397
221.1223
221.1222
307.2665
216.1162
361.5417
359.4692
359.4693
359.4694
359.4696
359.4697
311.2738
311.2758
362.6178
355.4186
299.2462
348.3852
362.6161
353.4116
353.4117
349.3902
310.2720
304.2580
344.3709
362.6256
362.6430
360.5112
356.4296
346.3787
361.5405
359.4851
359.4852
361.5884
362.6453
342.3628
231.1340
adk
rps13
rps11
rpoA
rpl17
truA
rpl13
alr
psaB
psaA
cbiG
lipA
glsF
rps12
rps7
fusA
tufA
rps10
pheA
rnhB
rne
cysH
nadB
aroK
rpaA
holB
Adenylate kinase
30S ribosomal protein S13
30S ribosomal protein S11
RNA polymerase alpha subunit
50S ribosomal protein L17
tRNA pseudouridine synthase A
50S ribosomal protein L13
HNH endonuclease family protein
putative alanine racemase
photosystem I P700 chlorophyll a apoprotein subuni
photosystem I P700 chlorophyll a apoprotein subuni
bifunctional cbiH protien and precorrin-3B C17-meth
lipoic acid synthetase
Ferredoxin-dependent glutamate synthase, Fd-GO
30S ribosomal protein S12
30S ribosomal protein S7
elongation factor EF-G
elongation factor EF-Tu
30S ribosomal protein S10
ATP-dependent protease La (LON) domain
Chorismate mutase-Prephenate dehydratase
ribonuclease HII
ribonuclease E
conserved hypothetical protein
Phosphoadenosine phosphosulfate reductase
putative NADH dehydrogenase, transport associated
possible sodium transporter, Trk family
putative potassium channel, VIC family
possible Fe-S oxidoreductase
conserved hypothetical protein
putative L-aspartate oxidase
conserved hypothetical protein
possible Fe-S oxidoreductase
conserved hypothetical protein
conserved hypothetical protein
Shikimate kinase
possible Ribosome-binding factor A
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
two-component response regulator
DNA polymerase III, delta prime subunit
Thymidylate kinase
Table 2
Pag
ort191
ort552
ort572
ort502
ort501
ort676
ort213
4.3036
3.9926
1.1578
4.3056
5.9015
6.5207
9.7292
1
0
1
1
0
0
0
all3193
alr3823
all3822
alr0238
alr0241
asr3137
all3136
glr0715
glr2406
glr2669
gll0800
gll3009
gsl4394
gll2924
0132
0133
0134
0135
0138
0140
0141
1992
1993
1994
1995
1998
2000
2001
387.10
479.20
479.118
506.153
506.157
475.30
475.75
131.820
133.1188
133.1298
133.1299
133.1302
133.1185
132.1104
0154
0155
0156
0157
0160
0163
0164
slr0823
slr0448
slr0947
slr1510
sll1848
ssr1425
sll0825
tll1525
tlr1103
tll2364
tlr0844
tlr0042
tsl2457
tlr0715
122.7024
119.4331
119.4162
115.2555
115.2561
108.1011
108.928
2240
2245
2246
2247
2250
2253
2254
232.2777
232.852
232.853
232.1666
232.1669
232.2723
232.2722
253.1646
361.5486
361.5773
358.4622
360.5035
238.1449
238.1438
ort323
ort129
ort554
ort471
ort469
ort130
ort131
ort238
ort470
ort472
ort473
ort466
ort386
ort656
ort536
ort229
ort293
ort207
ort132
ort442
ort393
ort509
ort133
ort337
ort478
ort134
ort019
ort463
ort285
ort639
ort567
ort136
4.9792
4.1746
2.8047
4.0972
2.5841
6.5891
4.9200
3.5926
1.9638
4.3225
2.6506
2.5004
4.9342
2.3165
5.4007
5.5545
4.0812
6.2389
7.1534
7.5926
7.2132
2.6452
7.6884
6.7481
4.3700
6.0225
9.8344
8.5661
5.9917
3.7358
5.3363
5.7803
0
1
1
1
1
0
0
1
1
1
1
1
0
1
1
1
1
0
0
0
1
1
0
0
1
0
0
0
0
1
1
0
alr1833
all1732
all3953
alr3956
alr3957
alr3399
all0783
asl2551
alr0226
alr0225
alr0224
alr0223
alr0222
all3794
alr0989
alr3201
all1736
alr2505
all3354
alr0033
all3859
all0273
all0271
all0270
all0269
all0268
all3717
all2091
all4677
all1549
alr0522
all0745
glr1744
glr1522
glr1340
glr0218
glr0219
glr1857
glr0789
gsl4037
gll0652
gll0653
gll0654
gll1584
glr3012
glr2758
gll1251
glr4402
glr1588
gll4384
glr2927
gll1578
gll3682
glr1233
gll1243
gll1242
glr0883
glr0884
glr4279
gll0888
glr2452
glr2748
glr0073
glr3866
0143
0145
0147
0149
0150
0151
0153
0154
0157
0158
0159
0160
0161
0164
0167
0168
0169
0170
0171
0176
0178
0180
0182
0183
0184
0185
0187
0188
0189
0191
0193
0194
2003
2005
2007
2009
2010
2011
2013
2014
2017
2018
2019
2020
2021
2027
2038
2040
2043
2045
2048
2059
2061
2063
2065
2066
2067
2068
2070
2073
2074
2111
2109
2108
474.11
434.47
429.39
429.15
429.16
506.25
492.56
454.36
401.40
401.39
401.38
401.36
401.35
505.109
372.14
507.107
434.46
461.80
498.130
382.6
502.154
480.45
480.47
480.48
480.49
480.50
507.173
372.1
501.94
405.29
456.45
482.87
135.1845
135.1987
135.1843
135.1990
135.1991
135.1994
128.445
131.930
128.471
128.470
128.469
128.468
127.342
130.657
136.2802
136.2296
135.2057
129.562
134.1484
133.1232
131.823
136.2313
136.2315
136.2316
136.2317
136.2318
135.2189
126.243
135.2184
133.1254
134.1412
134.1410
0166
0168
0170
0172
0173
0174
0176
0177
0181
0182
0183
0184
0185
0188
0191
0193
0194
0195
0196
0201
0203
0205
0207
0208
0209
0210
0212
0213
0214
0217
0219
0220
slr1255
slr1623
sll0998
slr0844
slr0331
slr1530
slr2141
ssl0564
sll0522
sll0521
sll0520
sll0519
sll0401
slr0543
sll0901
slr0525
slr1783
slr0387
sll1144
slr1518
slr1238
sll1865
slr0053
slr0054
slr0055
slr2005
sll0502
slr0936
sll1615
slr1325
slr1629
slr0267
tll1560
tll0447
tlr1206
tll0720
tll0719
tll1658
tll1771
tsl1865
tlr0670
tlr0669
tlr0668
tlr0667
tlr2393
tll2475
tll0586
tll0451
tlr1263
tlr0115
tlr2072
tlr2196
tlr0908
tll0527
tlr1585
tlr1586
tlr1471
tlr1472
tll0826
tll1713
tlr0961
tll0584
tll1538
tlr1507
120.4690
104.483
119.4263
118.3907
118.3909
101.110
122.6918
121.5189
122.6296
122.6295
122.6294
122.6291
122.6290
118.3575
121.5847
122.7900
121.5862
120.4669
120.5159
120.4641
120.4545
109.1139
118.3814
118.3815
118.3817
113.2053
120.4920
117.3252
107.835
122.7534
115.2450
113.1916
2256
2258
2260
2262
2263
2265
2267
2268
2271
2272
2273
2274
2275
2280
2285
2287
2289
2291
2298
2307
2309
2311
2313
2314
2315
2316
2319
2320
2322
2324
2326
2327
232.3649
232.4194
232.729
232.726
232.725
232.2324
232.1916
232.4368
232.1655
232.1654
232.1653
232.1652
232.1651
232.886
232.1879
232.2784
232.4192
232.4323
232.2107
232.1574
232.814
232.1720
232.1718
232.1717
232.1716
232.1715
232.2460
232.2050
232.960
232.3830
232.1850
232.3505
197.948
288.2236
294.2363
354.4160
349.3920
272.1946
361.5476
195.935
362.6240
362.6239
362.6238
362.6237
249.1600
314.2817
287.2211
318.2923
283.2148
253.1650
187.843
360.4882
360.5226
362.6601
362.6503
362.6504
362.6505
362.6506
360.5034
267.1863
351.4010
360.4975
362.6597
361.5504
ort494
ort457
ort407
ort546
2.7961
6.9532
8.1217
5.7483
0
0
0
0
all4131
alr0477
alr3936
all4272
glr2313
gll1671
gll3423
gll3080
0195
0197
0198
0199
2106
2101
2100
2094
501.49
494.62
498.63
460.17
134.1572
131.814
134.1570
136.2715
0221
0223
0224
0225
slr0394
slr1656
sll1713
slr1418
tll2268
tlr1809
tll2266
tll0579
113.2055
107.798
116.2830
119.4239
2329
2333
2334
2337
232.4647
232.1819
232.746
232.5080
361.5524
361.5832
361.5256
356.4298
Online Supporting Information
ycf3
radA
rpaB
plsX
plsC
ycf34
crtB,
pys
rbcR
ndhF
ndhD
ndhE
ndhG
ndhI
ndhA
gltA
trpB
purE
menA
gshB
prfB
dgkA
pabA
argS
nadC
spoT
rluD
cbbK,
pgk
murG
hisC
pyrD
cyanobacterial conserved hypothetical
putative DNA repair protein RadA
two-component response regulator
fatty acid/phospholipid synthesis protein PlsX
putative 1-acyl-sn-glycerol-3-phosphate acyltransfera
conserved hypothetical protein
Poly A polymerase family
phytoene synthases
conserved hypothetical protein
putative Rubisco transcriptional regulator
NADH dehydrogenase I chain 5 (or L)
NADH dehydrogenase I chain 4 (or M)
conserved hypothetical protein
conserved hypothetical protein
possible transcriptional regulator
NADH dehydrogenase I chain 4L or K
NADH dehydrogenase I chain 6 (or J)
NADH dehydrogenase I chain I (or NdhI)
NADH dehydrogenase I chain 1 (or H)
citrate synthase
Tryptophan synthase, beta chain:Pyridoxal-5'-pho
Phosphoribosylaminoimidazole carboxylase
Possible magnesium protoprophyrin IX methyltra
two-component response regulator
NifS-like aminotransferase class-V
conserved hypothetical protein
1,4-dihydroxy-2-naphthoate (DHNA) octaprenyltrans
putative glutathione synthetase
peptide chain release factor RF-2
conserved hypothetical protein
possible diacylglycerol kinase
para-aminobenzoate synthase component II
conserved hypothetical protein
arginyl-tRNA synthetase
Nicotinate-nucleotide pyrophosphorylase:Quinolinate
putative thiophen / furan oxidation protein
guanosine-3',5'-bis(diphosphate) 3'-diphosphatase
putative pseudouridylate synthase specific to ribos
conserved hypothetical protein
phosphoglycerate kinase
Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNA
Aminotransferases class-I
Dihydroorotate dehydrogenase
Table 2
ort577
ort575
ort576
ort477
ort348
ort227
ort018
ort310
ort371
ort209
ort010
ort375
ort374
ort137
ort600
ort377
ort260
ort675
ort195
ort138
ort205
ort376
ort028
ort549
ort214
ort311
ort507
ort140
ort342
ort024
ort141
ort618
ort016
ort451
ort672
ort559
ort651
Pag
2.5367
4.3721
0.9899
2.8070
3.8010
6.1653
5.7029
8.2410
3.6018
3.7407
3.8672
4.4045
5.6959
4.3567
5.3708
3.1755
9.2830
3.9285
7.1840
7.8596
6.1241
5.7757
3.5136
2.7609
7.6399
5.6999
4.8985
8.4568
1.7110
6.9624
8.7828
4.8520
3.1965
6.6821
2.5809
13.9041
3.0887
1
1
1
1
1
0
0
0
1
1
1
0
0
0
0
1
0
1
0
0
0
0
1
1
0
0
0
0
1
0
0
1
1
0
1
0
1
alr5303
alr5302
alr5300
alr5299
all3538
alr4515
alr2073
all1754
alr1396
alr3402
alr2418
all4607
all4608
alr1600
all0579
alr3561
all1717
all1318
all2473
all5037
alr0512
all4609
all2436
alr5000
alr5095
alr0520
alr3593
all1610
alr1742
alr2057
all4804
all4802
alr4798
all4316
alr3716
alr4961
all2072
glr1602
glr1601
glr1599
glr0830
gll2121
glr4178
glr4034
glr2134
gll2342
glr0710
gll2348
glr0246
glr3531
glr3015
gll2632
gll0881
glr0727
glr2919
glr0783
glr2334
gll2594
glr3530
gll1928
glr1524
gll3037
glr2580
gll1501
gll3147
glr4264
gll3278
glr3297
gsl0434
glr2933
gll3738
glr4236
gll0271
gll1463
Online Supporting Information
0201
0202
0204
0205
0208
0209
0050
0049
0048
0046
0044
1668
1669
1670
1673
1675
0659
1682
1030
1001
1684
1687
1688
1689
1691
1694
1696
1698
1704
1705
0654
1706
1707
1709
1712
1713
1716
2091
2090
2088
2087
2083
2082
2135
2136
2139
2148
2157
2169
2170
2171
2175
2177
2184
2191
2208
1386
2211
2215
2216
2219
2222
2237
2245
2247
2255
2257
2258
2259
2261
2264
2270
2271
2274
411.3
411.2
354.24
354.23
484.29
509.255
363.8
444.19
363.7
506.28
421.16
504.31
504.30
462.66
497.165
428.31
459.8
453.50
465.20
457.38
474.55
504.29
484.71
489.91
475.87
439.48
479.95
483.38
421.19
454.58
493.57
493.58
493.101
452.50
457.64
299.2
472.49
127.338
127.337
127.334
127.333
127.371
132.1045
135.2038
136.2706
136.2626
129.618
132.1049
135.1874
135.1873
129.564
129.579
125.166
136.2378
136.2871
132.1092
132.999
133.1320
131.813
128.447
135.2004
128.461
136.2535
135.1613
134.1443
129.523
129.634
136.2427
136.2526
136.2576
136.2444
132.1076
135.1745
136.2571
0227
0228
0230
0231
0235
0236
0054
0053
0052
0050
0048
1829
1830
1831
1834
1836
1841
1844
1502
1187
1847
1851
1852
1853
1855
1858
1862
1864
1871
1872
1873
1874
1875
1878
1881
1882
1885
sll1746
sll1745
sll1743
sll1742
slr0752
sll1770
sll1883
slr0553
sll1435
sll1852
sll0362
slr0293
slr0879
slr0580
sll1244
sll0202
sll1209
slr0557
sll1937
sll0157
sll1005
sll0171
slr1720
sll1443
slr0527
sll0378
sll0290
slr1652
sll0170
slr1559
sll1737
sll1767
slr0585
sll0657
slr1844
sll1520
sll1172
tlr0298
tlr0297
tlr0295
tlr0294
tlr0658
tlr2242
tll1911
tlr0898
tlr2394
tlr0267
tll2103
tll1603
tlr1678
tlr2020
tlr2413
tlr0535
tll0857
tlr1503
tlr0192
tlr2433
tlr0809
tll0745
tll1144
tll0768
tlr1732
tlr0144
tlr0213
tll2039
tlr1733
tll0590
tlr1073
tlr1279
tlr0712
tll0971
tll0184
tll1899
tll1227
121.5561
121.5560
121.5558
121.5557
121.6150
121.5999
122.7762
116.2769
122.6707
101.113
120.4504
118.3757
118.3755
103.292
103.305
121.6104
112.1647
121.5381
110.1285
122.6983
118.3754
114.2154
115.2408
104.403
119.4300
101.169
108.973
118.3658
112.1833
109.1223
120.4830
120.4831
114.2209
122.7016
121.5477
118.3637
121.6077
2340
2341
2343
2344
2348
2349
2353
2354
2356
2358
2360
2374
2375
2376
2378
2382
2389
2396
2401
2402
2418
2425
2426
2428
2431
2475
2495
2497
2508
2509
2510
2511
2513
2516
2522
2523
2526
232.1507
232.1506
232.1504
232.1503
232.2417
232.2284
232.2033
232.4174
232.2836
232.2327
232.4120
232.1698
232.1697
232.3083
232.4219
232.2439
232.4204
232.1906
232.4292
232.1257
232.1842
232.1696
232.4140
232.1228
232.1322
232.1848
232.2076
232.3091
232.4186
232.2021
232.1045
232.1043
232.1039
232.5124
232.2490
232.1198
232.2032
241.1484
241.1483
188.861
188.860
243.1513
318.2921
225.1272
357.4421
317.2913
362.6188
131.388
314.2812
358.4606
233.1366
330.3277
349.3904
361.5402
339.3526
361.5768
328.3193
354.4155
254.1664
353.4089
88.174
362.6090
361.5933
362.6491
342.3653
362.6498
336.3438
361.5451
361.5452
141.464
360.5013
314.2814
295.2380
362.6189
rpl12
rpl10
rpl11
nusG
eno
argJ
coaE
gatB
alaS
gcvP
gcsH
rpl9
gidA
valS
gcvT
aspS
pyrG
cobA
ppk
dnaK2
aroE
ycf60
rps6
argG
mraY
uvrA
recN
thrC
50S ribosomal protein L7/L12
50S ribosomal protein L10
50S ribosomal protein L11
transcription antitermination protein, NusG
Enolase
possible kinase
glutamate N-acetyltransferase / ornithine N-acetyltran
putative dephospho-CoA kinase
glutamyl-tRNA (Gln) amidotransferase subunit B
Nucleoside diphosphate kinase
Alanyl-tRNA synthetase
Glycine cleavage system P-protein
putative Glycine cleavage H-protein
conserved hypothetical protein
50S ribosomal protein L9
glucose inhibited division protein A
Putative DNA ligase
valyl-tRNA synthetase
Ferric uptake regulator family
conserved hypothetical protein
MazG family protein
putative Glycine cleavage T-protein (aminomethyl tra
Aspartyl-tRNA synthetase:GAD domain:tRNA syn
Glutamine amidotransferase class-I:CTP synthase
possible ATPase
putative uroporphyrin-III c-methyltransferase
putative polyphosphate kinase
conserved hypothetical protein
Molecular chaperone DnaK2, heat shock protein h
Shikimate / quinate 5-dehydrogenase
conserved hypothetical protein
30S ribosomal protein S6
Argininosuccinate synthase
Putative phospho-N-acetylmuramoyl-pentapeptide-tra
excinuclease ABC subunit A
putative DNA repair protein
threonine synthase
Figure legends
Page 19
Fig. 6. Representative backbone tree topologies and other hypotheses used in the ShimodairaHasegawa test. In order to determine which of the above topologies best represent the
evolutionary history of the conserved protein families, we performed a Shimodaira-Hasegawa
(SH) test (74) in which the fitness of a particular topology to the 682 sequence alignments was
analyzed. To aid the comparison, we also generated topologies that display alternative placement
of SCO and TEL with minor or no changes in topologies of the conserved clades (T6-T10), as
well as topologies that break the conserved clades at random (T11-T15). Note that only 2~3%
topological divergence is displayed. Species abbreviations as in Table 1.
Fig. 7. Compatibility of tree topologies to the orthologous datasets. The SH tests show the
number of datasets accepting (black bars) or rejecting (grey bars) each of the 15 topologies at the
5% significance level. The SH tests indicated that almost all (97.5% to 99.6%) of the datasets
support topologies T1-T5 at the 95% confidence level (P=0.95), whereas much fewer datasets
support topologies T6-T11, and T11-T15 were strongly rejected by most of the datasets. While
this analysis corroborated the main stream as discerned through genomic approaches, it was
inadequate in choosing a unique, preferable topology to other similar ones. This result suggests
that artificial paralogs or genes potentially obtained by LGT may thwart the establishment of
organismal relationships based on plural consensus of individual gene phylogenies.
Online Supporting Information
Figure 6
Page 20
SSU rRNA
Concatenated proteins
16S_NJ/ML/MP;
NJ_γ
NJD; NJJ; NJK;QP
ANA
AVA
NPU
TER
CWA
SYN
PMM
PMS
PMT
SYW
SCO
TEL
GVI
T1
ANA
AVA
NPU
TER
CWA
SYN
TEL
PMM
PMS
PMT
SYW
SCO
GVI
T2
Consensus and supertree
ProtML; ML_consensus;
ML_supertree
ANA
AVA
NPU
TER
CWA
SYN
PMM
PMS
PMT
SYW
SCO
TEL
GVI
T3
NJ_consensus
NJ_supertree
ANA
AVA
NPU
TER
CWA
SYN
TEL
SCO
SYW
PMT
PMS
PMM
GVI
T4
ANA
AVA
NPU
TER
CWA
SYN
TEL
SYW
PMT
PMS
PMM
SCO
GVI
T5
Other hypotheses
SYW
PMT
PMS
PMM
ANA
AVA
NPU
SYN
CWA
SCO
TER
TEL
GVI
T6
ANA
AVA
NPU
TER
CWA
SYN
SCO
TEL
PMM
PMS
PMT
SYW
GVI
T7
SYW
PMT
PMM
PMS
SCO
TEL
SYN
NPU
AVA
ANA
CWA
TER
GVI
T11
ANA
AVA
NPU
TER
CWA
SYN
SCO
SYW
PMT
PMS
PMM
TEL
GVI
T8
SYN
NPU
ANA
AVA
TER
CWA
SCO
TEL
PMT
PMM
PMS
SYW
GVI
T12
ANA
AVA
NPU
TER
CWA
SYN
TEL
SCO
PMM
PMS
PMT
SYW
GVI
T9
ANA
AVA
NPU
TEL
CWA
SYN
SYW
PMM
PMT
SCO
PMS
TER
GVI
T13
SYW
PMS
PMT
PMM
SCO
SYN
CWA
ANA
AVA
NPU
TEL
TER
GVI
T10
ANA
AVA
NPU
CWA
TER
PMT
PMS
PMM
SYW
SCO
TEL
SYN
GVI
T14
CWA
SCO
SYN
PMT
PMS
SYW
ANA
AVA
NPU
TER
TEL
PMM
GVI
T15
Shi & Falkowski, SI Fig. 6
Online Supporting Information
Figure 7
Page 21
700
Number of orthologs
650
600
550
500
150
100
50
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Tree topologies
Shi & Falkowski, SI Fig. 7
Online Supporting Information