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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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SynteView main window. The SynteView main window consists of a menu bar, a toolbar (on the left), a central panel which displays synteny relationships between a reference species and the compared ones, and a bottom panel, which shows the extent to which the reference species genes are conserved in blocks found in other species.
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Figure 4: SynteView main window. The SynteView main window consists of a menu bar, a toolbar (on the left), a central panel which displays synteny relationships between a reference species and the compared ones, and a bottom panel, which shows the extent to which the reference species genes are conserved in blocks found in other species.

Mentions: The whole set of synteny data that was stored in SynteBase was further examined using SynteView. This tool was designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. For example, the user can choose the set of genomes to be studied by defining either an array of species names or a taxonomic sampling. The procedure used to visualize synteny between a reference species s1 and a set of species (s2, s3, s4, s5) is straightforward. The user first chooses a reference species, in the "select reference genome panel" by selecting nodes in the species tree (Fig. 3). Clicking on a node produces a list of all the species that are its leaves (right panel). Then, the reference species is chosen by clicking on the species name in this list. Next, the set of compared species is determined by means of the "select compared species" tab (Fig. 3). As previously noted, the user browses the taxonomic tree of prokaryotes. When the user clicks on one node of the tree (e.g. Enterobacteriales), all the descendants of this node appear in the bottom panel. To choose one or several species, a drag and drop of the selected names will move the corresponding species into the right panel. This can be repeated several times, until the required set of species is selected. When this step is accomplished, clicking on the "Start data retrieval process" button on the bottom of the panel will launch the visualization step. The speed of this process depends on the number and nature of the chosen species. Once the retrieval process is completed, all regions of each compared genome become accessible for visualization in a scrollable window using the following features as shown in Fig. 4. Each line corresponds to a genome. The first line from the top (light blue background) shows gene adjacency in the chromosome of the reference species. Dark blue (positive DNA strand) and yellow (negative strand) rectangles stand for genes belonging to a synteny block that is conserved in at least one other species. Gray rectangles are genes of this reference genome that do not have any POGs in the set of compared genomes. Respective gene names are labeled on each rectangle. The following lines contain the different species that are compared to the reference genome. SynteView automatically sorts the chosen species by their taxonomic proximity to the reference genome. For each gene of the reference genome, columns contain the orthologous genes belonging to a synteny block found to be conserved in the different analyzed genomes with their respective names. The same color code (blue or yellow) helps to discriminate the strand of their respective location on each genome. The number of genes present in a block is displayed when the cursor is run over this block. Note that synteny blocks in compared genomes are defined exclusively with respect to the gene order in the reference genome. Thus, in a SynteView window of synteny blocks, the apparent proximity in compared genomes does not imply that they are as physically close in these genomes as their POGs are in the reference genome. By opening the Settings panel (to do so, click on the "settings" button in the left toolbar menu) the user accesses a Dialog box where it is possible to modify various default parameters. For example, clicking on the "Database" tab allows the user to choose the retrieval mode (database or web service). Once these various parameters have been customized, it is possible to navigate along the reference genome to estimate the density of the synteny blocks present in the other genomes. For example, and as expected, comparing E. coli with the other gammaproteobacteria reveals a rather high density of gene conservation. The bottom blue background shape portrays this rate of conservation in the compared genomes as a histogram (Fig. 4).


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

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

SynteView main window. The SynteView main window consists of a menu bar, a toolbar (on the left), a central panel which displays synteny relationships between a reference species and the compared ones, and a bottom panel, which shows the extent to which the reference species genes are conserved in blocks found in other species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: SynteView main window. The SynteView main window consists of a menu bar, a toolbar (on the left), a central panel which displays synteny relationships between a reference species and the compared ones, and a bottom panel, which shows the extent to which the reference species genes are conserved in blocks found in other species.
Mentions: The whole set of synteny data that was stored in SynteBase was further examined using SynteView. This tool was designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. For example, the user can choose the set of genomes to be studied by defining either an array of species names or a taxonomic sampling. The procedure used to visualize synteny between a reference species s1 and a set of species (s2, s3, s4, s5) is straightforward. The user first chooses a reference species, in the "select reference genome panel" by selecting nodes in the species tree (Fig. 3). Clicking on a node produces a list of all the species that are its leaves (right panel). Then, the reference species is chosen by clicking on the species name in this list. Next, the set of compared species is determined by means of the "select compared species" tab (Fig. 3). As previously noted, the user browses the taxonomic tree of prokaryotes. When the user clicks on one node of the tree (e.g. Enterobacteriales), all the descendants of this node appear in the bottom panel. To choose one or several species, a drag and drop of the selected names will move the corresponding species into the right panel. This can be repeated several times, until the required set of species is selected. When this step is accomplished, clicking on the "Start data retrieval process" button on the bottom of the panel will launch the visualization step. The speed of this process depends on the number and nature of the chosen species. Once the retrieval process is completed, all regions of each compared genome become accessible for visualization in a scrollable window using the following features as shown in Fig. 4. Each line corresponds to a genome. The first line from the top (light blue background) shows gene adjacency in the chromosome of the reference species. Dark blue (positive DNA strand) and yellow (negative strand) rectangles stand for genes belonging to a synteny block that is conserved in at least one other species. Gray rectangles are genes of this reference genome that do not have any POGs in the set of compared genomes. Respective gene names are labeled on each rectangle. The following lines contain the different species that are compared to the reference genome. SynteView automatically sorts the chosen species by their taxonomic proximity to the reference genome. For each gene of the reference genome, columns contain the orthologous genes belonging to a synteny block found to be conserved in the different analyzed genomes with their respective names. The same color code (blue or yellow) helps to discriminate the strand of their respective location on each genome. The number of genes present in a block is displayed when the cursor is run over this block. Note that synteny blocks in compared genomes are defined exclusively with respect to the gene order in the reference genome. Thus, in a SynteView window of synteny blocks, the apparent proximity in compared genomes does not imply that they are as physically close in these genomes as their POGs are in the reference genome. By opening the Settings panel (to do so, click on the "settings" button in the left toolbar menu) the user accesses a Dialog box where it is possible to modify various default parameters. For example, clicking on the "Database" tab allows the user to choose the retrieval mode (database or web service). Once these various parameters have been customized, it is possible to navigate along the reference genome to estimate the density of the synteny blocks present in the other genomes. For example, and as expected, comparing E. coli with the other gammaproteobacteria reveals a rather high density of gene conservation. The bottom blue background shape portrays this rate of conservation in the compared genomes as a histogram (Fig. 4).

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