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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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Schematic diagram of established and proposed contributions to the eukaryotic genome. The eukaryotic genome is proposed to contain genes from many different sources. The nucleocytoplasm was proposed to have evolved from an archaeal-like ancestor [47,48]. This archaeal ancestor was either an organism that branched off before the most recent common ancestor of the today's archaea (as in the traditional rRNA-based tree of life that contains a monophyletic archaeal clade [15]), or it might have been more specifically related to the crenarchaeota (as in the eocyte proposal [16], which results in the archaea being a paraphyletic grouping). Other well-corroborated contributions are the mitochondria and chloroplasts [49], which evolved from bacterial endosymbionts, and which contributed many genes to the nuclear genome [50]. Additional contributions were proposed to have originated from now-extinct organisms [26,27], such as the 'chronocyte', and through many single-gene transfers from many different sources that might have been ingested as food by early eukaryotes [25].
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Figure 6: Schematic diagram of established and proposed contributions to the eukaryotic genome. The eukaryotic genome is proposed to contain genes from many different sources. The nucleocytoplasm was proposed to have evolved from an archaeal-like ancestor [47,48]. This archaeal ancestor was either an organism that branched off before the most recent common ancestor of the today's archaea (as in the traditional rRNA-based tree of life that contains a monophyletic archaeal clade [15]), or it might have been more specifically related to the crenarchaeota (as in the eocyte proposal [16], which results in the archaea being a paraphyletic grouping). Other well-corroborated contributions are the mitochondria and chloroplasts [49], which evolved from bacterial endosymbionts, and which contributed many genes to the nuclear genome [50]. Additional contributions were proposed to have originated from now-extinct organisms [26,27], such as the 'chronocyte', and through many single-gene transfers from many different sources that might have been ingested as food by early eukaryotes [25].

Mentions: Genes in eukaryotes are proposed to represent different contributions from different organisms (Figure 6). If appropriate representatives of the bacterial and archaeal domains are chosen, the genes that were acquired from different putative contributors to the eukaryotic lineage can be differentiated through different tree topologies. Here we attempt to partition a eukaryotic genome with respect to the different contributions. We selected the genome quintet containing one well-annotated eukaryote (Saccharomyces cerevisiae), two archaea representing two archaeal kingdoms (the euryarchaeote Archaeoglobus fulgidus and the crenarchaeote Sulfolobus solfataricus), and two bacteria (the alpha-proteobacterium Rhodobacter capsulatus and the Gram-positive bacterium Bacillus subtilis).


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

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

Schematic diagram of established and proposed contributions to the eukaryotic genome. The eukaryotic genome is proposed to contain genes from many different sources. The nucleocytoplasm was proposed to have evolved from an archaeal-like ancestor [47,48]. This archaeal ancestor was either an organism that branched off before the most recent common ancestor of the today's archaea (as in the traditional rRNA-based tree of life that contains a monophyletic archaeal clade [15]), or it might have been more specifically related to the crenarchaeota (as in the eocyte proposal [16], which results in the archaea being a paraphyletic grouping). Other well-corroborated contributions are the mitochondria and chloroplasts [49], which evolved from bacterial endosymbionts, and which contributed many genes to the nuclear genome [50]. Additional contributions were proposed to have originated from now-extinct organisms [26,27], such as the 'chronocyte', and through many single-gene transfers from many different sources that might have been ingested as food by early eukaryotes [25].
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Related In: Results  -  Collection

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Figure 6: Schematic diagram of established and proposed contributions to the eukaryotic genome. The eukaryotic genome is proposed to contain genes from many different sources. The nucleocytoplasm was proposed to have evolved from an archaeal-like ancestor [47,48]. This archaeal ancestor was either an organism that branched off before the most recent common ancestor of the today's archaea (as in the traditional rRNA-based tree of life that contains a monophyletic archaeal clade [15]), or it might have been more specifically related to the crenarchaeota (as in the eocyte proposal [16], which results in the archaea being a paraphyletic grouping). Other well-corroborated contributions are the mitochondria and chloroplasts [49], which evolved from bacterial endosymbionts, and which contributed many genes to the nuclear genome [50]. Additional contributions were proposed to have originated from now-extinct organisms [26,27], such as the 'chronocyte', and through many single-gene transfers from many different sources that might have been ingested as food by early eukaryotes [25].
Mentions: Genes in eukaryotes are proposed to represent different contributions from different organisms (Figure 6). If appropriate representatives of the bacterial and archaeal domains are chosen, the genes that were acquired from different putative contributors to the eukaryotic lineage can be differentiated through different tree topologies. Here we attempt to partition a eukaryotic genome with respect to the different contributions. We selected the genome quintet containing one well-annotated eukaryote (Saccharomyces cerevisiae), two archaea representing two archaeal kingdoms (the euryarchaeote Archaeoglobus fulgidus and the crenarchaeote Sulfolobus solfataricus), and two bacteria (the alpha-proteobacterium Rhodobacter capsulatus and the Gram-positive bacterium Bacillus subtilis).

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