Eric Zuchantke

Friedrich-Loeffler-Institut

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Herbert Tomaso

Friedrich-Loeffler-Institut

Helmut Hotzel

Friedrich-Loeffler-Institut

Anne Busch

Jena University Hospital

Sascha Al Dahouk

Federal Institute for Risk Assessment

Kerstin Neubert

Federal Institute for Risk Assessment

Holger Brendebach

Federal Institute for Risk Assessment

Burkhard Malorny

Federal Institute for Risk Assessment

Robert Maximilian Leidenfrost

Federal Institute for Occupational Safety and Health

Timo Homeier

Friedrich-Loeffler-Institut

Knut Reinert

Freie Universität Berlin

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Friedrich-Loeffler-Institut

Federal Institute for Risk Assessment

Freie Universität Berlin

Federal Institute for Health Protection of Consumers and Veterinary Medicine

Hochschule Mittweida

Max Planck Institute for Molecular Genetics

Animal Health Institute

Lower Saxony State Office for Consumer Protection and Food Safety

Robert Koch Institute

Universität der Bundeswehr München

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Additional file 13 of Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Figshare (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke

Additional file 13: Supplementary Fig. 13. Effects of coverage on NGA50 values and errrors in Flye/P ilon assemblies.

Francisella

10.6084/m9.figshare.17007198

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Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

BMC Genomics (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Röbbe Wünschiers Josephine Grützke

We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation "short-read" and third-generation "long-read" sequencing methods.We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a "long-read first" approach.Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis.

Francisella

Pathogenicity island

Sequence assembly

Comparative Genomics

10.1186/s12864-021-08115-x

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Citations (4)

Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis

Frontiers in Microbiology (2018)

Anne Busch Prasad Thomas Eric Zuchantke Holger Brendebach Kerstin Neubert

Francisella (F.) tularensis is a highly virulent, Gram-negative bacterial pathogen and the causative agent of the zoonotic disease tularemia. Here, we generated, analyzed and characterized a high quality circular genome sequence of the F. tularensis subsp. holarctica strain 12T0050 that caused fatal tularemia in a hare. Besides the genomic structure, we focused on the analysis of oriC, unique to the Francisella genus and the first report on genomic DNA methylation of a Francisella strain. The high quality genome was used to establish and evaluate a diagnostic whole genome sequencing pipeline. A genotyping strategy for F. tularensis was developed using various bioinformatics tools for genotyping. Additionally, whole genome sequences of F. tularensis subsp. holarctica isolates isolated in the years 2008-2015 in Germany were generated. A phylogenetic analysis allowed to determine the genetic relatedness of these isolates and confirmed the highly conserved nature of F. tularensis subsp. holarctica.

Tularemia

Francisella

10.3389/fmicb.2018.00344

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Citations (12)

CyanoFactory Knowledge Base & Synthetic Biology - A Plea for Human Curated Bio-databases

Gabriel M. Kind Eric Zuchantke Röbbe Wünschiers

Plea

Base (topology)

10.5220/0005285802370242

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Citations (3)

Additional file 2 of Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Figshare (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke

Additional file 2: Supplementary Figure 2. Bivariate plot of log-transformed read length against base call quality with hexagonal bins and marginal histograms (NanoPlot) of raw reads a) PacBio and b) ONT.

Francisella

10.6084/m9.figshare.17007237

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Additional file 15 of Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Figshare (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke

Additional file 15: Supplementary Fig. 15. Effects of preprocessing on errors in hybrid assembl ies.

Francisella

10.6084/m9.figshare.17007204

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Additional file 19 of Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Figshare (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke

Additional file 19: Supplementary Table 1. Read statistic of raw data and preprocessed reads.

Francisella

10.6084/m9.figshare.17007219

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Semantic Tools for Forensics: Towards Finding Evidence in Short Messages

Michael Spranger Eric Zuchantke Dirk Labudde

Computer forensics

Network forensics

Source

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Additional file 20 of Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures

Figshare (2021)

Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke

Additional file 20: Supplementary Table 2. Performance of tested eight short-read assemblers in five isolates of F. tularensis.

Francisella

10.6084/m9.figshare.17007225

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High-Quality Genome Sequence of Bacillus anthracis Strain 14RA5914 Isolated during an Outbreak in Germany in 2014

Genome Announcements (2017)

Mandy C. Elschner Anne Busch Annette Schliephake Wolfgang Gaede Eric Zuchantke

Bacillus anthracis is a zoonotic agent causing anthrax, a notifiable disease in animals. The last anthrax outbreak among cattle in Germany occurred in April 2014 in Saxony-Anhalt. Here we report a high-quality genome sequence of the Bacillus anthracis strain 14RA5914 Dobichau isolated from the spleen of a dead cow.

Bacillus anthracis

Anthrax vaccines

Strain (injury)

10.1128/genomea.01002-17

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Citations (7)