EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Blom, Jochen; Albaum, Stefan P.; Doppmeier, Daniel; Pühler, Alfred; Vorhölter, Frank-Jörg; Zakrzewski, Martha; Goesmann, Alexander

doi:10.1186/1471-2105-10-154

Cited by 377 publications

(443 citation statements)

References 45 publications

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“…The core genome was calculated based on the presence of orthologous genes in all 17 genomes, determined by a reciprocal best BLAST hit using EDGAR (Blom et al, 2009) and a phylogenetic tree was generated from the sequence alignment of the core genome, as previously described (Trost et al, 2012). The nucleotide sequences of MLST genes from all 17 genomes were extracted using MLST 1.5 (Larsen et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are major barriers to recombination through recognition of invading nucleic acids, such as phage and plasmids, and promoting their degredation through the action of CRISPR associated (Cas) proteins. The genomic comparison of 17 Corynebacterium diphtheriae strains led to the identification of three novel CRISPR-Cas system variants, based on the Type II (Type II-C) or type I-E systems. The type II-C system was the most common (11/17 isolates) but it lacked the csn2 and cas4 genes that are involved in spacer acquisition. We also identified that this variant type II-C CRISPR-Cas system is present in other bacteria, and the first system was recently characterized in Neisseria meningitidis. In the remaining isolates, the type II-C system was replaced by a variant of type I-E (I-E-a), where the repeat arrays are inserted between the cas3 and cse1 genes. Three isolates with the type II-C system also possess an additional variant of type I-E (I-E-b), elsewhere in the genome, that exhibits a novel divergent gene organization within the cas operon. The nucleotide sequences of the palindromic repeats and the cas1 gene were phylogenetically incongruent to the core genome. The G+C content of the systems is lower (46.0-49.5 mol%) than the overall DNA G+C content (53 mol%), and they are flanked by mobile genetic elements, providing evidence that they were acquired in three independent horizontal gene transfer events. The majority of spacers lack identity with known phage or plasmid sequences, indicating that there is an unexplored reservoir of corynebacteriophages and plasmids. These novel CRISPR-Cas systems may represent a unique mechanism for spacer acquisitions and defence against invading DNA.

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Section: Methodsmentioning

confidence: 99%

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

2013

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“…Blast ring images were generated using BRIG (Alikhan et al, 2011). Genome comparisons were performed in EDGAR (Blom et al, 2009). This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/ GenBank under the accession JZLL00000000.…”

Section: Rrf4 Strainmentioning

confidence: 99%

Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica

et al. 2015

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The Alphaproteobacterium Rhizobium radiobacter F4 (RrF4) was originally characterized as an endofungal bacterium in the beneficial endophytic Sebacinalean fungus Piriformospora indica. Although attempts to cure P. indica from RrF4 repeatedly failed, the bacterium can easily be grown in pure culture. Here, we report on RrF4's genome and the beneficial impact the free-living bacterium has on plants. In contrast to other endofungal bacteria, the genome size of RrF4 is not reduced. Instead, it shows a high degree of similarity to the plant pathogenic R. radiobacter (formerly: Agrobacterium tumefaciens) C58, except vibrant differences in both the tumor-inducing (pTi) and the accessor (pAt) plasmids, which can explain the loss of RrF4's pathogenicity. Similar to its fungal host, RrF4 colonizes plant roots without host preference and forms aggregates of attached cells and dense biofilms at the root surface of maturation zones. RrF4-colonized plants show increased biomass and enhanced resistance against bacterial leaf pathogens. Mutational analysis showed that, similar to P. indica, resistance mediated by RrF4 was dependent on the plant's jasmonate-based induced systemic resistance (ISR) pathway. Consistent with this, RrF4-and P. indica-induced pattern of defense gene expression were similar. In clear contrast to P. indica, but similar to plant growth-promoting rhizobacteria, RrF4 colonized not only the root outer cortex but also spread beyond the endodermis into the stele. On the basis of our findings, RrF4 is an efficient plant growth-promoting bacterium.

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“…These contribute to the gene diversity of X. fastidiosa and provide potential avenues for horizontal gene transfer (HGT) both within and between species. Due to the ability of HGT to confer new phenotypes on Venn diagram for the number of predicted coding sequences that are shared and unique from representative genomes of subspecies multiplex, fastidiosa, and pauca calculated with EDGAR (Blom et al 2009), using a protein-protein BLAST e-value cutoff of 10 -6 and 70 % amino acid identity bacteria and modify their ecological niche, there is intense interest in exploring the contribution of these elements to the distinct virulence traits of different isolates, including the ability to colonize novel host plants (Moreira et al 2005;Nunes et al 2003).…”

Section: Mobile Elementsmentioning

confidence: 99%

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

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Labroussaa

Shapiro

et al. 2014

Genomics of Plant-Associated Bacteria

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EDGAR: A software framework for the comparative analysis of prokaryotic genomes

Cited by 377 publications

References 45 publications

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

Novel configurations of type I and II CRISPR–Cas systems in Corynebacterium diphtheriae

Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

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