Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures
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 o...
Guardado en:
| Autores principales: | , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
BMC
2021
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/c30de5e7596e46d2b4a57628b591e229 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:c30de5e7596e46d2b4a57628b591e229 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:c30de5e7596e46d2b4a57628b591e2292021-11-14T12:26:50ZTesting assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures10.1186/s12864-021-08115-x1471-2164https://doaj.org/article/c30de5e7596e46d2b4a57628b591e2292021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08115-xhttps://doaj.org/toc/1471-2164Abstract 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.Kerstin NeubertEric ZuchantkeRobert Maximilian LeidenfrostRoebbe WuenschiersJosephine GrützkeBurkhard MalornyHolger BrendebachSascha Al DahoukTimo HomeierHelmut HotzelKnut ReinertHerbert TomasoAnne BuschBMCarticleFrancisella pathogenicity islandInsertion sequencesHigh-throughput sequencingShort-read assemblyHybrid assemblyIon Torrent’s ion S5BiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-21 (2021) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Francisella pathogenicity island Insertion sequences High-throughput sequencing Short-read assembly Hybrid assembly Ion Torrent’s ion S5 Biotechnology TP248.13-248.65 Genetics QH426-470 |
| spellingShingle |
Francisella pathogenicity island Insertion sequences High-throughput sequencing Short-read assembly Hybrid assembly Ion Torrent’s ion S5 Biotechnology TP248.13-248.65 Genetics QH426-470 Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke Burkhard Malorny Holger Brendebach Sascha Al Dahouk Timo Homeier Helmut Hotzel Knut Reinert Herbert Tomaso Anne Busch Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| description |
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. |
| format |
article |
| author |
Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke Burkhard Malorny Holger Brendebach Sascha Al Dahouk Timo Homeier Helmut Hotzel Knut Reinert Herbert Tomaso Anne Busch |
| author_facet |
Kerstin Neubert Eric Zuchantke Robert Maximilian Leidenfrost Roebbe Wuenschiers Josephine Grützke Burkhard Malorny Holger Brendebach Sascha Al Dahouk Timo Homeier Helmut Hotzel Knut Reinert Herbert Tomaso Anne Busch |
| author_sort |
Kerstin Neubert |
| title |
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| title_short |
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| title_full |
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| title_fullStr |
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| title_full_unstemmed |
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| title_sort |
testing assembly strategies of francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures |
| publisher |
BMC |
| publishDate |
2021 |
| url |
https://doaj.org/article/c30de5e7596e46d2b4a57628b591e229 |
| work_keys_str_mv |
AT kerstinneubert testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT ericzuchantke testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT robertmaximilianleidenfrost testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT roebbewuenschiers testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT josephinegrutzke testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT burkhardmalorny testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT holgerbrendebach testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT saschaaldahouk testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT timohomeier testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT helmuthotzel testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT knutreinert testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT herberttomaso testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures AT annebusch testingassemblystrategiesoffrancisellatularensisgenomestoinferanevolutionaryconservationanalysisofgenomicstructures |
| _version_ |
1718429253991661568 |