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. 2014 Jan 17;9(1):e86318.
doi: 10.1371/journal.pone.0086318. eCollection 2014.

CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips

Hamed Heydari  1 , Cheuk Chuen Siow  2 , Mui Fern Tan  2 , Nick S Jakubovics  3 , Wei Yee Wee  4 , Naresh V R Mutha  2 , Guat Jah Wong  4 , Mia Yang Ang  4 , Amir Hessam Yazdi  5 , Siew Woh Choo  4
Affiliations

CoryneBase: Corynebacterium genomic resources and analysis tools at your fingertips

Hamed Heydari et al. PLoS One. .

Abstract

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. To facilitate the ongoing research of corynebacteria, a specialized central repository and analysis platform for the corynebacterial research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. Here we present CoryneBase, a genomic database for Corynebacterium with diverse functionality for the analysis of genomes aimed to provide: (1) annotated genome sequences of Corynebacterium where 165,918 coding sequences and 4,180 RNAs can be found in 27 species; (2) access to comprehensive Corynebacterium data through the use of advanced web technologies for interactive web interfaces; and (3) advanced bioinformatic analysis tools consisting of standard BLAST for homology search, VFDB BLAST for sequence homology search against the Virulence Factor Database (VFDB), Pairwise Genome Comparison (PGC) tool for comparative genomic analysis, and a newly designed Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomic analysis. CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics. It is publicly available at http://corynebacterium.um.edu.my/.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Feature diagram showing the overall functionalities of CoryneBase.
Screenshots of CoryneBase web pages with five distinct features accessible from the navigation bar on top: browse, search, tools, genome browser, and download. Four bioinformatic tools are incorporated in CoryneBase: standard BLAST, VFDB BLAST, PGC, and PathoProT.
Figure 2
Figure 2. Pairwise genome comparison.
Circos-generated circular representation of comparing two complete genomes with 50% genome identity threshold: C. pseudotuberculosis FRC41 (left) and C. ulcerans 0102 (right). Colored links connect a subset of genomic region pairs that are homologous between the two genomes. Label number 1 represents genomic locus for tox-positive prophage while 2 and 3 for other prophages on the chromosome of C. ulcerans 0102.
Figure 3
Figure 3. Pathogenomics profiling.
Clustered heat map generated by PathoProT comparing all the genomes of Corynebacterium with 50% sequence identity and completeness thresholds. The data are sorted by hierarchical clustering on both strains and virulence genes to bring similarities together. Cluster relationships are indicated by dendrograms along the left and top of the heat map, and the state of virulence genes being present or absent may indicate functional relationships among strains.
See this image and copyright information in PMC

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Grants and funding

This work was supported by UM High Impact Research Grant UM-MOHE UM.C/HIR/MOHE/08 from the Ministry of Higher Education Malaysia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.