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PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas.

Moustafa A, Bhattacharya D - BMC Evol. Biol. (2008)

Bottom Line: Using PhyloSort, we identified 897 Chlamydomonas genes of putative cyanobacterial origin, of which 531 had bootstrap support values >/= 50% for the grouping of the algal and cyanobacterial homologs.PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events.In our application, we demonstrate that cyanobacteria account for 3.5-6% of the protein-coding genes in the nuclear genome of Chlamydomonas.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Iowa, Interdisciplinary Program in Genetics, 456 Biology Building, Iowa City, Iowa 52242, USA. ahmed-moustafa@uiowa.edu

ABSTRACT

Background: Phylogenomic pipelines generate a large collection of phylogenetic trees that require manual inspection to answer questions about gene or genome evolution. A notable application of phylogenomics is to photosynthetic organelle (plastid) endosymbiosis. In the case of primary endosymbiosis, a heterotrophic protist engulfed a cyanobacterium, giving rise to the first photosynthetic eukaryote. Plastid establishment precipitated extensive gene transfer from the endosymbiont to the nuclear genome of the 'host'. Estimating the magnitude of this endosymbiotic gene transfer (EGT) and determining the functions of the prokaryotic genes remain controversial issues. We used phylogenomics to study EGT in the model green alga Chlamydomonas reinhardtii. To facilitate this procedure, we developed PhyloSort to rapidly search large collection of trees for monophyletic relationships. Here we present PhyloSort and its application to estimating EGT in Chlamydomonas.

Results: PhyloSort is an open-source tool to sort phylogenetic trees by searching for user specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units in a phylogenomic context. Using PhyloSort, we identified 897 Chlamydomonas genes of putative cyanobacterial origin, of which 531 had bootstrap support values >/= 50% for the grouping of the algal and cyanobacterial homologs.

Conclusion: PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events. In our application, we demonstrate that cyanobacteria account for 3.5-6% of the protein-coding genes in the nuclear genome of Chlamydomonas.

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Screenshot of the Reference Taxonomy tree in PhyloSort (Windows XP) that can be used to select the groups of taxa.
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Related In: Results  -  Collection

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Figure 2: Screenshot of the Reference Taxonomy tree in PhyloSort (Windows XP) that can be used to select the groups of taxa.

Mentions: To begin the analysis, the hypothesized monophyletic taxa are selected from a pool of taxa. This pool of taxa can be loaded as a simple list from a plain text file. Alternatively, a tree can be loaded that acts as a taxonomy reference for organizing the taxa in a phylogenetic format (Figure 2). Finally, if no list is loaded or no reference tree exists, the program will unite all taxa in all trees into a single non-redundant list of taxa.


PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of Chlamydomonas.

Moustafa A, Bhattacharya D - BMC Evol. Biol. (2008)

Screenshot of the Reference Taxonomy tree in PhyloSort (Windows XP) that can be used to select the groups of taxa.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2254586&req=5

Figure 2: Screenshot of the Reference Taxonomy tree in PhyloSort (Windows XP) that can be used to select the groups of taxa.
Mentions: To begin the analysis, the hypothesized monophyletic taxa are selected from a pool of taxa. This pool of taxa can be loaded as a simple list from a plain text file. Alternatively, a tree can be loaded that acts as a taxonomy reference for organizing the taxa in a phylogenetic format (Figure 2). Finally, if no list is loaded or no reference tree exists, the program will unite all taxa in all trees into a single non-redundant list of taxa.

Bottom Line: Using PhyloSort, we identified 897 Chlamydomonas genes of putative cyanobacterial origin, of which 531 had bootstrap support values >/= 50% for the grouping of the algal and cyanobacterial homologs.PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events.In our application, we demonstrate that cyanobacteria account for 3.5-6% of the protein-coding genes in the nuclear genome of Chlamydomonas.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Iowa, Interdisciplinary Program in Genetics, 456 Biology Building, Iowa City, Iowa 52242, USA. ahmed-moustafa@uiowa.edu

ABSTRACT

Background: Phylogenomic pipelines generate a large collection of phylogenetic trees that require manual inspection to answer questions about gene or genome evolution. A notable application of phylogenomics is to photosynthetic organelle (plastid) endosymbiosis. In the case of primary endosymbiosis, a heterotrophic protist engulfed a cyanobacterium, giving rise to the first photosynthetic eukaryote. Plastid establishment precipitated extensive gene transfer from the endosymbiont to the nuclear genome of the 'host'. Estimating the magnitude of this endosymbiotic gene transfer (EGT) and determining the functions of the prokaryotic genes remain controversial issues. We used phylogenomics to study EGT in the model green alga Chlamydomonas reinhardtii. To facilitate this procedure, we developed PhyloSort to rapidly search large collection of trees for monophyletic relationships. Here we present PhyloSort and its application to estimating EGT in Chlamydomonas.

Results: PhyloSort is an open-source tool to sort phylogenetic trees by searching for user specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units in a phylogenomic context. Using PhyloSort, we identified 897 Chlamydomonas genes of putative cyanobacterial origin, of which 531 had bootstrap support values >/= 50% for the grouping of the algal and cyanobacterial homologs.

Conclusion: PhyloSort can be applied to quantify the number of genes that support different evolutionary hypotheses such as a taxonomic classification or endosymbiotic or horizontal gene transfer events. In our application, we demonstrate that cyanobacteria account for 3.5-6% of the protein-coding genes in the nuclear genome of Chlamydomonas.

Show MeSH