StaphyloBase: a specialized genomic resource for the staphylococcal research community

Abstract

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses. Database URL: http://staphylococcus.um.edu.my/.

Figure 1.

Real-time search function. (A) Users can search using different parameters. For example, they can search by keywords and a list of matches from the database will be displayed at the bottom in real-time. (B) Example of search output.

Figure 2.

PGC workflow and automation for comparing two user-defined staphylococcal genomes. This includes the parsing of user-defined parameters and text files containing information, such as karyotype (in Circos, karyotypes are typically chromosomes or sequence contigs or clones in biological context), links, histograms and bands by Perl and Python scripts to create a Circos.conf file for displaying the aligned genomes with Circos.

Figure 3.

The influence of different cut-offs for the Merge Threshold (MT) and Link Threshold (LT). As a case study, the genomes of S. aureus strain 11819–97 and S. aureus strain 118 were compared using PGC tool. Each half circle (either left or right) represents each separate genome/assembly. The coloured links show the homologous regions in the two selected genomes. We can clearly observe how different user-defined thresholds affect the display of the two aligned genomes. (A) Different cut-offs for MT. Parameters: Genome Identity—95% and LT—1000 bp were used for all three plots. (B) Different cut-offs for LT. Parameters: Genome Identity—95% and MT—0 bp were used for all three plots.

Figure 4.

Heat map showing clusters of the selected staphylococcal strains based on their virulence gene profiles. The columns represent the staphylococcal strains, whereas the rows represent the predicted virulence genes. A red box indicates the presence of the virulence gene in the corresponding strain. In contrast, a black box indicates absence. Through this clustering, it is easy to visualize the common virulence genes (e.g. nuc) across the selected staphylococcal strains/species, strain-specific virulence genes (e.g. sec, sel for strain S. epidermidis FR1909) and species-specific virulence genes (e.g. hysA, esaA essA, and essB are specific to all selected S. aureus).

Figure 5.

Browser panel showing a genomic region associated with a gene encoding diaminopimelate epimerase and its neighbouring genes. CDS, DNA and RNA are shown in different tracks.