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EDGAR: a software framework for the comparative analysis of prokaryotic genomes.

Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A - BMC Bioinformatics (2009)

Bottom Line: As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach.Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database.EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. jblom@cebitec.uni-bielefeld.de

ABSTRACT

Background: The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.

Results: To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" - was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy.

Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de, where the precomputed data sets can be browsed.

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Synteny of the Xanthomonas chromosomes. Synteny of the Xanthomonas chromosomes. In order to monitor the conservation of gene order among the Xanthomonas chromosomes, pairwise synteny plots were generated with EDGAR, where the position of each CDS of the chromosome given on the X axis is plotted against the position of its homologue in the second chromosome given on the Y axis. Identical chromosomes result in a diagonal plot. The names of the analyzed chromosome pairs are given on top of each plot. Among the Xcc and Xca chromosomes there are few chromosomal rearrangements, some of which indicate large-scale inversion events. The number of rearrangements increases rather subtly when the Xca/Xcv chromosomes are compared to Xcc strains. A substantial increase in rearrangements becomes obvious for Xoc BLS256 when compared to Xcc B100, while the gene order seems almost disintegrated in Xoo 10331 (similar data for the other Xoo chromosomes not shown). While synteny analysis is restricted to complete genome data for obvious reasons, other tools like the phylogenetic tree analysis of the Venn diagrams are also available for draft genome data.
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Figure 6: Synteny of the Xanthomonas chromosomes. Synteny of the Xanthomonas chromosomes. In order to monitor the conservation of gene order among the Xanthomonas chromosomes, pairwise synteny plots were generated with EDGAR, where the position of each CDS of the chromosome given on the X axis is plotted against the position of its homologue in the second chromosome given on the Y axis. Identical chromosomes result in a diagonal plot. The names of the analyzed chromosome pairs are given on top of each plot. Among the Xcc and Xca chromosomes there are few chromosomal rearrangements, some of which indicate large-scale inversion events. The number of rearrangements increases rather subtly when the Xca/Xcv chromosomes are compared to Xcc strains. A substantial increase in rearrangements becomes obvious for Xoc BLS256 when compared to Xcc B100, while the gene order seems almost disintegrated in Xoo 10331 (similar data for the other Xoo chromosomes not shown). While synteny analysis is restricted to complete genome data for obvious reasons, other tools like the phylogenetic tree analysis of the Venn diagrams are also available for draft genome data.

Mentions: To get an overview on the true taxonomy of the sequenced Xanthomonas strains, the determined core genome data was used for a phylogenetic analysis. The genome divergence was quantified with EDGAR using a similar approach to one which recently proved to be of value for eukaryotes [28]. The result can be displayed in a tree with two main branches: the first comprising almost all X. campestris genomes and the second with the genomes of the X. oryzae strains, which includes the genomes of X. axonopodis and of X. campestris pv. vesicatoria 85-10 in a separate branch (see Figure 3). In the X. campestris branch, all Xcc genomes were very close to each other and the genome of Xca 756C was only marginally more distant from these strains. The second branch was more heterogeneous. Beside the branch with Xac 306 and Xcv 85-10 the genome of Xoc BLS256 was more distant from the Xoo strains. This phylogenetic clustering was in good accordance with the phytopathogenicity of the Xanthomonas strains; the X. campestris strains, which were grouped together, are all pathogens of cruciferous plants, while the X. oryzae strains are pathogens of rice (Oryza sativa). Also, Xoc BLS256, which forms a distinct branch within this group, causes bacterial leaf streak disease, while the Xoo strains provoke bacterial blight. Xcv and Xac that diverge from the second branch leading to the rice pathogens, affect pepper and citrus plants, respectively. The phylogenetic tree was derived from the core genome that comprised 2,156 CDS and thus less than half the genome of each Xanthomonas strain. To shed more light on the relation of the Xanthomonads, the synteny of genome pairs was plotted, which gave a rough survey on the conservation of gene order between individual strains (Figure 6). For the analysis Xcc B100 was set as a reference. The comparisons show that the gene order of Xcc B100, which despite some striking inversions was generally well conserved in the Xcc and Xca chromosomes, was increasingly disintegrated along the phylogenetic tree that indicates their divergence (Figure 4). While there was considerable conservation in the Xca/Xcv chromosomes, the number of rearrangements increased dramatically in comparison to Xoc, with the gene order almost comminuted in Xoo. Such chromosomal rearrangements have been linked to IS elements [35,38], mobile genetic elements that were found frequently in Xanthomonas genomes, with numbers ranging from 58 in Xcv 85-10 to 267 in Xoo PXO99A [35,37].


EDGAR: a software framework for the comparative analysis of prokaryotic genomes.

Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A - BMC Bioinformatics (2009)

Synteny of the Xanthomonas chromosomes. Synteny of the Xanthomonas chromosomes. In order to monitor the conservation of gene order among the Xanthomonas chromosomes, pairwise synteny plots were generated with EDGAR, where the position of each CDS of the chromosome given on the X axis is plotted against the position of its homologue in the second chromosome given on the Y axis. Identical chromosomes result in a diagonal plot. The names of the analyzed chromosome pairs are given on top of each plot. Among the Xcc and Xca chromosomes there are few chromosomal rearrangements, some of which indicate large-scale inversion events. The number of rearrangements increases rather subtly when the Xca/Xcv chromosomes are compared to Xcc strains. A substantial increase in rearrangements becomes obvious for Xoc BLS256 when compared to Xcc B100, while the gene order seems almost disintegrated in Xoo 10331 (similar data for the other Xoo chromosomes not shown). While synteny analysis is restricted to complete genome data for obvious reasons, other tools like the phylogenetic tree analysis of the Venn diagrams are also available for draft genome data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2696450&req=5

Figure 6: Synteny of the Xanthomonas chromosomes. Synteny of the Xanthomonas chromosomes. In order to monitor the conservation of gene order among the Xanthomonas chromosomes, pairwise synteny plots were generated with EDGAR, where the position of each CDS of the chromosome given on the X axis is plotted against the position of its homologue in the second chromosome given on the Y axis. Identical chromosomes result in a diagonal plot. The names of the analyzed chromosome pairs are given on top of each plot. Among the Xcc and Xca chromosomes there are few chromosomal rearrangements, some of which indicate large-scale inversion events. The number of rearrangements increases rather subtly when the Xca/Xcv chromosomes are compared to Xcc strains. A substantial increase in rearrangements becomes obvious for Xoc BLS256 when compared to Xcc B100, while the gene order seems almost disintegrated in Xoo 10331 (similar data for the other Xoo chromosomes not shown). While synteny analysis is restricted to complete genome data for obvious reasons, other tools like the phylogenetic tree analysis of the Venn diagrams are also available for draft genome data.
Mentions: To get an overview on the true taxonomy of the sequenced Xanthomonas strains, the determined core genome data was used for a phylogenetic analysis. The genome divergence was quantified with EDGAR using a similar approach to one which recently proved to be of value for eukaryotes [28]. The result can be displayed in a tree with two main branches: the first comprising almost all X. campestris genomes and the second with the genomes of the X. oryzae strains, which includes the genomes of X. axonopodis and of X. campestris pv. vesicatoria 85-10 in a separate branch (see Figure 3). In the X. campestris branch, all Xcc genomes were very close to each other and the genome of Xca 756C was only marginally more distant from these strains. The second branch was more heterogeneous. Beside the branch with Xac 306 and Xcv 85-10 the genome of Xoc BLS256 was more distant from the Xoo strains. This phylogenetic clustering was in good accordance with the phytopathogenicity of the Xanthomonas strains; the X. campestris strains, which were grouped together, are all pathogens of cruciferous plants, while the X. oryzae strains are pathogens of rice (Oryza sativa). Also, Xoc BLS256, which forms a distinct branch within this group, causes bacterial leaf streak disease, while the Xoo strains provoke bacterial blight. Xcv and Xac that diverge from the second branch leading to the rice pathogens, affect pepper and citrus plants, respectively. The phylogenetic tree was derived from the core genome that comprised 2,156 CDS and thus less than half the genome of each Xanthomonas strain. To shed more light on the relation of the Xanthomonads, the synteny of genome pairs was plotted, which gave a rough survey on the conservation of gene order between individual strains (Figure 6). For the analysis Xcc B100 was set as a reference. The comparisons show that the gene order of Xcc B100, which despite some striking inversions was generally well conserved in the Xcc and Xca chromosomes, was increasingly disintegrated along the phylogenetic tree that indicates their divergence (Figure 4). While there was considerable conservation in the Xca/Xcv chromosomes, the number of rearrangements increased dramatically in comparison to Xoc, with the gene order almost comminuted in Xoo. Such chromosomal rearrangements have been linked to IS elements [35,38], mobile genetic elements that were found frequently in Xanthomonas genomes, with numbers ranging from 58 in Xcv 85-10 to 267 in Xoo PXO99A [35,37].

Bottom Line: As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach.Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database.EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. jblom@cebitec.uni-bielefeld.de

ABSTRACT

Background: The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons.

Results: To support these studies EDGAR - "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" - was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy.

Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de, where the precomputed data sets can be browsed.

Show MeSH
Related in: MedlinePlus