ArticleBMC genomics2016
Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- Article
- Activity of Ethanolic and Supercritical Propolis Extracts inFrontiers in veterinary science · 2021Article
- Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures.BMC bioinformatics · 2020Article
- Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.Scientific reports · 2019Article
- Biogenic Silver Nanoparticles as a Post-surgical Treatment forFrontiers in microbiology · 2019Article
- riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.Nucleic acids research · 2018Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.Genome biology · 2016Article
- SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.BMC bioinformatics · 2016Article
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Authors and funding
16 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.
resultsIn this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.
conclusionIn conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.
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