Abstract
BackgroundYersinia 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.DescriptionTo 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.ConclusionsYersiniaBase 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0422-y) contains supplementary material, which is available to authorized users.
Highlights
Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica
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
Virulence genes in Yersinia By calculating the number of virulence genes presents in every strain, we found that Y. pestis and Y. pseudotuberculosis generally have more virulence genes than other species and the number of virulence genes in different strains is more consistent within these species compared to Y. enterocolitica and non-pathogenic Yersinia (Figure 3)
Summary
Yersinia is a genus of Gram-negative rod shaped bacteria belonging to the Enterobacteriaceae family. One of the features of this database is the PathoProT which has been developed in-house, with the intention of identifying the potential virulence markers in the Yersinia genus This comparative analysis platform will help users gain a deeper insight into the different species of Yersinia especially in the area of their pathogenicity. We used Python, Perl, BioPerl [35] and R languages to develop the PGC for comparing between two genomes through global alignment, PathoProT for generating heat map to visualize presence and absence of virulence genes in selected genomes and YersiniaTree to generate phylogenetic tree of the Yersinia strains based on their housekeeping genes and 16S rRNA The use of these three popular scripting languages allowed us to create complex pipelines, that perform back-end calculations, aided communications between the web server and the application server and easier transfer of data from the web server to the application server and vice versa.
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