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

BMC Genomics

Robert Maximilian Leidenfrost¹  Röbbe Wünschiers¹  Knut Reinert²  Kerstin Neubert³  Herbert Tomaso⁴  Helmut Hotzel⁴  Eric Zuchantke⁴  Anne Busch⁵  Timo Homeier⁶  Sascha Al Dahouk⁷  Josephine Grützke⁷  Burkhard Malorny⁷  Holger Brendebach⁷ 

[1] Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany;Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany;Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany;German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany;Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany;Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany;Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany;Friedrich-Loeffler-Institut, Institute of Epidemiology, Südufer, 10 17493, Greifswald, Insel Riems, Germany;German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany;

关键词: Francisella;    Insertion sequences;    High-throughput sequencing;    Short-read assembly;    Hybrid assembly;    Ion Torrent’s ion S5;    Illumina MiSeq;    Illumina HiSeq;    Pacific biosciences RS;    Oxford Nanopore technologies MinION;   

DOI  :  10.1186/s12864-021-08115-x

来源: Springer

【 摘 要 】

BackgroundWe 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.ResultsWe 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.ConclusionsGenomic 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.

【 授权许可】

CC BY