title: Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.
abstract: BACKGROUND
  Studies 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  In 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.
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Diego César Batista
authors.initials: DC
authors.lastname: Mariano
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Thiago de Jesus
authors.initials: Tde J
authors.lastname: Sousa
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Felipe Luiz
authors.initials: FL
authors.lastname: Pereira
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Flávia
authors.initials: F
authors.lastname: Aburjaile
authors.affiliation: Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, 721172, India.
authors.forename: Debmalya
authors.initials: D
authors.lastname: Barh
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Flávia
authors.initials: F
authors.lastname: Rocha
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Anne Cybelle
authors.initials: AC
authors.lastname: Pinto
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Syed Shah
authors.initials: SS
authors.lastname: Hassan
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Tessália Diniz Luerce
authors.initials: TD
authors.lastname: Saraiva
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Fernanda Alves
authors.initials: FA
authors.lastname: Dorella
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Alex Fiorini
authors.initials: AF
authors.lastname: de Carvalho
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Carlos Augusto Gomes
authors.initials: CA
authors.lastname: Leal
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Henrique César Pereira
authors.initials: HC
authors.lastname: Figueiredo
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Rommel Thiago Jucá
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil. vasco@icb.ufmg.br.
authors.forename: Vasco Ariston Carvalho
authors.initials: VA
authors.lastname: Azevedo
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D016925:Corynebacterium pseudotuberculosis / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D015723:Gene Library; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA; D012407:rRNA Operon / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial
keywords: Genomics; Mis-assembly; Optical mapping; Sequencing