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SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.

Lemoine F, Labedan B, Lespinet O - BMC Bioinformatics (2008)

Bottom Line: However, persistent synteny blocks are found when comparing more or less distant species.This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable.It is also possible to download sequences of genes belonging to these synteny blocks for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât, 400, 91405 Orsay Cedex, France. frederic.lemoine@igmors.u-psud.fr

ABSTRACT

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.

Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.

Conclusion: SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.

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Displaying operon conservation. Part A shows that the order of genes belonging to the histidine operon is well conserved in this set of proteobacterial genomes. Part B shows the contrasting low conservation of the neighboring rfb cluster. Note that there is an interval of 12 E. coli genes (in the reference species) between gene hisI in panel A and gene rfbC in panel B.
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Figure 5: Displaying operon conservation. Part A shows that the order of genes belonging to the histidine operon is well conserved in this set of proteobacterial genomes. Part B shows the contrasting low conservation of the neighboring rfb cluster. Note that there is an interval of 12 E. coli genes (in the reference species) between gene hisI in panel A and gene rfbC in panel B.

Mentions: Information about any annotated gene is immediately available by clicking on the corresponding rectangle. This opens, to the left of the window, the "gene information" panel (Fig. 4) in which, for the selected gene, its GenBank PID, its name, the species name and the replicon to which it belongs are given; the function of its product (if available), and its exact location on the chromosome are also mentioned. This information panel also contains a text field which permits simple queries such as a search for a protein function, a gene name or a PID in the analyzed genomes, as well as a search for synteny blocks containing at least x adjacent genes and having orthologous genes in at least y species. Moreover, clicking on a gene delivers complete information on its neighbors. For instance, it is possible to estimate the various levels of conservation of detected operons when comparing organisms separated by various taxonomic distances. While the operon histidine is rather well conserved in proteobacteria (Fig. 5, panel A), the neighboring clusters of genes involved in the O-specific lipopolysaccharide biosynthesis (rfb cluster) and the production of extracellular polysaccharide colanic acid (cluster wca), which are located at a short distance and on the other strand, are rapidly fragmented to a scarce number of 2–4 genes such as the rml genes in Pseudomonas aeruginosa (Fig. 5, panel B). In addition, clicking on the "get sequences" button in the information panel opens a dialog box. SynteView shows the sequence of the clicked gene in the first tab and that of its orthologues in the second tab in Fasta format. This further allows downloading of all these amino acid sequences for future work.


SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.

Lemoine F, Labedan B, Lespinet O - BMC Bioinformatics (2008)

Displaying operon conservation. Part A shows that the order of genes belonging to the histidine operon is well conserved in this set of proteobacterial genomes. Part B shows the contrasting low conservation of the neighboring rfb cluster. Note that there is an interval of 12 E. coli genes (in the reference species) between gene hisI in panel A and gene rfbC in panel B.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667195&req=5

Figure 5: Displaying operon conservation. Part A shows that the order of genes belonging to the histidine operon is well conserved in this set of proteobacterial genomes. Part B shows the contrasting low conservation of the neighboring rfb cluster. Note that there is an interval of 12 E. coli genes (in the reference species) between gene hisI in panel A and gene rfbC in panel B.
Mentions: Information about any annotated gene is immediately available by clicking on the corresponding rectangle. This opens, to the left of the window, the "gene information" panel (Fig. 4) in which, for the selected gene, its GenBank PID, its name, the species name and the replicon to which it belongs are given; the function of its product (if available), and its exact location on the chromosome are also mentioned. This information panel also contains a text field which permits simple queries such as a search for a protein function, a gene name or a PID in the analyzed genomes, as well as a search for synteny blocks containing at least x adjacent genes and having orthologous genes in at least y species. Moreover, clicking on a gene delivers complete information on its neighbors. For instance, it is possible to estimate the various levels of conservation of detected operons when comparing organisms separated by various taxonomic distances. While the operon histidine is rather well conserved in proteobacteria (Fig. 5, panel A), the neighboring clusters of genes involved in the O-specific lipopolysaccharide biosynthesis (rfb cluster) and the production of extracellular polysaccharide colanic acid (cluster wca), which are located at a short distance and on the other strand, are rapidly fragmented to a scarce number of 2–4 genes such as the rml genes in Pseudomonas aeruginosa (Fig. 5, panel B). In addition, clicking on the "get sequences" button in the information panel opens a dialog box. SynteView shows the sequence of the clicked gene in the first tab and that of its orthologues in the second tab in Fasta format. This further allows downloading of all these amino acid sequences for future work.

Bottom Line: However, persistent synteny blocks are found when comparing more or less distant species.This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable.It is also possible to download sequences of genes belonging to these synteny blocks for further studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et Microbiologie, Université Paris Sud XI, CNRS UMR 8621, Bât, 400, 91405 Orsay Cedex, France. frederic.lemoine@igmors.u-psud.fr

ABSTRACT

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.

Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.

Conclusion: SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.

Show MeSH