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Visualization of the phylogenetic content of five genomes using dekapentagonal maps.

Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP - Genome Biol. (2004)

Bottom Line: The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures.If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus.Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.

ABSTRACT
The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.

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Bootstrap support map from extended QuintOPs of five photosynthetic genomes. For notations see legend to Figure 2.
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Figure 3: Bootstrap support map from extended QuintOPs of five photosynthetic genomes. For notations see legend to Figure 2.

Mentions: For the genome quintet of photosynthetic organisms that we initially analyzed in [5], both the posterior probability map and the bootstrap support map show that a plurality of datasets support three tree topologies: numbers 5, 10, and 15 (see Figures 2 and 3). The extended datasets (Figure 3) provide a more realistic illustration of the reliability of the individual analyses than the map based on the ML-mapping approach (Figure 2). While the plurality consensus is still discernable in Figure 3, many datasets do not map close to any of the vertices, suggesting that these sets of orthologous proteins cannot discriminate between at least some of the possible phylogenies. One might be tempted to conclude that not much phylogenetic information survived and that the apparent conflicts [5] were due to a lack of resolution only [13]. However, each five-taxon tree has two internal branches, that is, two bipartitions that contain phylogenetic information. The smallest quantum of phylogenetic information is the individual bipartition, not the resolved tree topology. In the five-taxon case a bipartition can be viewed as a partially unresolved tree where two taxa are grouped together, while the relationship among the other three taxa remains unresolved. An analysis of the possible bipartitions is a better way to gauge the extent of surviving phylogenetic information and the conflict between the individual datasets than dekapentagonal maps. We summarize the support for the 10 possible bipartitions in the form of a histogram (Figure 4). The bipartition corresponding to the plurality consensus signal for trees 5, 10 and 15 is labeled as bipartition A. This bipartition has plurality support. Xiong et al.[14] reported that enzymes involved in (bacterio)chlorophyll biosynthesis are supporting the topology that in the dekapentagonal map is labeled as topology 13. Topology 13 corresponds to two bipartitions labeled as E and G in Figure 4. In our set of 188 QuintOPs, only a few members of the chlorophyll biosynthesis pathway are present: bchB/chlB, bchL/chlL and chlM. The other members of the chlorophyll biosynthesis pathway were not picked up because of the strict requirements imposed on the QuintOP assembly, that is, the requirement that the open reading frames (ORFs) that form a QuintOP mutually pick up each other in all five genomes as top-scoring BLAST hits. The reason that some members of the chlorophyll biosynthetic pathways are not assembled into QuintOPs is that there are multiple paralogous genes present in some of those genomes (especially in the Chlorobium and Chloroflexus genomes), and these prevent proper QuintOPs from being formed. We manually compiled the extended datasets for bchH/chlH, bchI/chlI, bchD/chlD, bchN/chlN genes and calculated the bootstrap support values for bipartitions A, E and G with different phylogenetic methods (Figure 5). In all cases the members of the photosynthetic pathway do not support the plurality bipartition, but significantly support the bipartitions reported by Xiong et al. [14]. This suggests that the genes from the chlorophyll biosynthetic pathway have a phylogenetic history different from the apparent plurality consensus.


Visualization of the phylogenetic content of five genomes using dekapentagonal maps.

Zhaxybayeva O, Hamel L, Raymond J, Gogarten JP - Genome Biol. (2004)

Bootstrap support map from extended QuintOPs of five photosynthetic genomes. For notations see legend to Figure 2.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC395770&req=5

Figure 3: Bootstrap support map from extended QuintOPs of five photosynthetic genomes. For notations see legend to Figure 2.
Mentions: For the genome quintet of photosynthetic organisms that we initially analyzed in [5], both the posterior probability map and the bootstrap support map show that a plurality of datasets support three tree topologies: numbers 5, 10, and 15 (see Figures 2 and 3). The extended datasets (Figure 3) provide a more realistic illustration of the reliability of the individual analyses than the map based on the ML-mapping approach (Figure 2). While the plurality consensus is still discernable in Figure 3, many datasets do not map close to any of the vertices, suggesting that these sets of orthologous proteins cannot discriminate between at least some of the possible phylogenies. One might be tempted to conclude that not much phylogenetic information survived and that the apparent conflicts [5] were due to a lack of resolution only [13]. However, each five-taxon tree has two internal branches, that is, two bipartitions that contain phylogenetic information. The smallest quantum of phylogenetic information is the individual bipartition, not the resolved tree topology. In the five-taxon case a bipartition can be viewed as a partially unresolved tree where two taxa are grouped together, while the relationship among the other three taxa remains unresolved. An analysis of the possible bipartitions is a better way to gauge the extent of surviving phylogenetic information and the conflict between the individual datasets than dekapentagonal maps. We summarize the support for the 10 possible bipartitions in the form of a histogram (Figure 4). The bipartition corresponding to the plurality consensus signal for trees 5, 10 and 15 is labeled as bipartition A. This bipartition has plurality support. Xiong et al.[14] reported that enzymes involved in (bacterio)chlorophyll biosynthesis are supporting the topology that in the dekapentagonal map is labeled as topology 13. Topology 13 corresponds to two bipartitions labeled as E and G in Figure 4. In our set of 188 QuintOPs, only a few members of the chlorophyll biosynthesis pathway are present: bchB/chlB, bchL/chlL and chlM. The other members of the chlorophyll biosynthesis pathway were not picked up because of the strict requirements imposed on the QuintOP assembly, that is, the requirement that the open reading frames (ORFs) that form a QuintOP mutually pick up each other in all five genomes as top-scoring BLAST hits. The reason that some members of the chlorophyll biosynthetic pathways are not assembled into QuintOPs is that there are multiple paralogous genes present in some of those genomes (especially in the Chlorobium and Chloroflexus genomes), and these prevent proper QuintOPs from being formed. We manually compiled the extended datasets for bchH/chlH, bchI/chlI, bchD/chlD, bchN/chlN genes and calculated the bootstrap support values for bipartitions A, E and G with different phylogenetic methods (Figure 5). In all cases the members of the photosynthetic pathway do not support the plurality bipartition, but significantly support the bipartitions reported by Xiong et al. [14]. This suggests that the genes from the chlorophyll biosynthetic pathway have a phylogenetic history different from the apparent plurality consensus.

Bottom Line: The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures.If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus.Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA.

ABSTRACT
The methods presented here summarize phylogenetic relationships of genomes in visually appealing and informative figures. Dekapentagonal maps depict phylogenetic information for orthologous genes present in five genomes, and provide a pre-screen for putatively horizontally transferred genes. If the majority of individual gene phylogenies are unresolved, bipartition histograms provide a means of uncovering and analyzing the plurality consensus. Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods.

Show MeSH