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

BMC Genomics

Roebbe Wuenschiers¹  Robert Maximilian Leidenfrost¹  Knut Reinert²  Kerstin Neubert²  Helmut Hotzel³  Eric Zuchantke³  Anne Busch³  Herbert Tomaso³  Timo Homeier⁴  Burkhard Malorny⁵  Josephine Grützke⁵  Holger Brendebach⁵  Sascha Al Dahouk⁵ 

[1] Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences;Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science;Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses;Friedrich-Loeffler-Institut, Institute of Epidemiology;German Federal Institute for Risk Assessment;

关键词: Francisella pathogenicity island;    Insertion sequences;    High-throughput sequencing;    Short-read assembly;    Hybrid assembly;    Ion Torrent’s ion S5;   

DOI  :  10.1186/s12864-021-08115-x

来源: DOAJ

【 摘 要 】

Abstract Background 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. Results 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. Conclusions 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.

【 授权许可】

Unknown