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YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, Heydari H, Wee WY, Wong GJ, Choo SW - BMC Bioinformatics (2015)

Bottom Line: The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species.In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase.We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.

ABSTRACT

Background: Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity.

Description: To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

Conclusions: YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .

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Related in: MedlinePlus

Phylogenetic tree constructed by from virulence gene profiles with PathoProT.
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Fig2: Phylogenetic tree constructed by from virulence gene profiles with PathoProT.

Mentions: Apart from the trees generated based on gyrB a separate tree was constructed based on the virulence profiles of Y. pestis and Y. pseudotuberculosis strains using the PathoProT (Figure 2). Even in the tree by PathoProT (Figure 2), we found that Y. pestis and Y. pseudotuberculosis formed a cluster that was clearly separated from Y. enterocolitica and non-pathogenic Yersinia which was similar to that observed in both the trees based on gyrB. This similarity in the clustering pattern, suggests that the housekeeping genes and virulence genes of Y. pestis and Y. pseudotuberculosis evolved in a similar pathway and are distinct from the other Yersinia species. These results were in agreement with a recently published report suggesting that Y. pestis and Y. pseudotuberculosis are close relatives, however Y. enterocolitica shows diametric separation with most environmental species occupying intermediate branching positions between these two clusters [57,58]. The tree also indicates that Y. pestis Angola is the first among the Y. pestis strains to branch out from the closest common ancestor Y. pseudotuberculosis YPIII. This observation is supported by a recently published report, which stated that Y. pestis Angola belongs to one of the most ancient Y. pestis lineages sequenced to date, possessing genome characteristics which are intermediate between Y. pseudotuberculosis and the modern day Y. pestis [59]. These data suggest that Y. pestis is highly similar to Y. pseudotuberculosis genetically and the virulence genes that were lost or acquired did not cause it to diverge far from its ancestor. However, Y. pestis has undergone gene reduction and has accumulated pseudogenes since its emergence from Y. pseudotuberculosis [60,61].Figure 2


YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, Heydari H, Wee WY, Wong GJ, Choo SW - BMC Bioinformatics (2015)

Phylogenetic tree constructed by from virulence gene profiles with PathoProT.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384384&req=5

Fig2: Phylogenetic tree constructed by from virulence gene profiles with PathoProT.
Mentions: Apart from the trees generated based on gyrB a separate tree was constructed based on the virulence profiles of Y. pestis and Y. pseudotuberculosis strains using the PathoProT (Figure 2). Even in the tree by PathoProT (Figure 2), we found that Y. pestis and Y. pseudotuberculosis formed a cluster that was clearly separated from Y. enterocolitica and non-pathogenic Yersinia which was similar to that observed in both the trees based on gyrB. This similarity in the clustering pattern, suggests that the housekeeping genes and virulence genes of Y. pestis and Y. pseudotuberculosis evolved in a similar pathway and are distinct from the other Yersinia species. These results were in agreement with a recently published report suggesting that Y. pestis and Y. pseudotuberculosis are close relatives, however Y. enterocolitica shows diametric separation with most environmental species occupying intermediate branching positions between these two clusters [57,58]. The tree also indicates that Y. pestis Angola is the first among the Y. pestis strains to branch out from the closest common ancestor Y. pseudotuberculosis YPIII. This observation is supported by a recently published report, which stated that Y. pestis Angola belongs to one of the most ancient Y. pestis lineages sequenced to date, possessing genome characteristics which are intermediate between Y. pseudotuberculosis and the modern day Y. pestis [59]. These data suggest that Y. pestis is highly similar to Y. pseudotuberculosis genetically and the virulence genes that were lost or acquired did not cause it to diverge far from its ancestor. However, Y. pestis has undergone gene reduction and has accumulated pseudogenes since its emergence from Y. pseudotuberculosis [60,61].Figure 2

Bottom Line: The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species.In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase.We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia. shiyangtan@gmail.com.

ABSTRACT

Background: Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity.

Description: To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica.

Conclusions: YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .

Show MeSH
Related in: MedlinePlus