Abstract
As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ) for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species.
Highlights
BackgroundIn February 2016 the Genomes OnLine Database counted 52,366 prokaryotic sequencing projects, representing more than 65% of all available sequencing projects [1]
In step 2 the remaining group A-open reading frames (ORFs) (= A-diagnostic marker genes (DMGs)) are compared to the group B genome sequences. This is done in order to identify A-DMGs having a high quality hit in B genomes, which were not discarded in step 1 as a consequence of frameshifts and inconsistent gene calling of genomes
BlAst Diagnostic Gene findEr (BADGE) is an easy-to-use and fast comparative genomics tool to answer the simple but often asked question: How can I differentiate my bacteria at the gene level and which genes are responsible for a specific phenotype? We show a straightforward procedure, from phenotyping, genome assembly as well as annotation and the usage of BADGE up to a diagnostic marker gene PCR assay, making comparative genomics a means to an end
Summary
BackgroundIn February 2016 the Genomes OnLine Database counted 52,366 prokaryotic sequencing projects, representing more than 65% of all available sequencing projects [1]. The number of generation sequencing (NGS) projects will increase in the future as sequencing technologies like single molecule real time sequencing (SMRT) produce high quality data at decreasing
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