Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002

BMC Genomics

Research Article

Debmalya Barh¹  Rommel Thiago Jucá Ramos²  Artur Silva²  Anne Cybelle Pinto³  Diego César Batista Mariano³  Tessália Diniz Luerce Saraiva³  Flávia Rocha³  Vasco Ariston Carvalho Azevedo³  Flávia Aburjaile³  Syed Shah Hassan³  Thiago de Jesus Sousa³  Carlos Augusto Gomes Leal⁴  Henrique César Pereira Figueiredo⁴  Fernanda Alves Dorella⁴  Alex Fiorini de Carvalho⁴  Felipe Luiz Pereira⁴ 

[1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, 721172, Purba Medinipur, WB, India;Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil;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;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;

关键词: Genomics;    Sequencing;    Optical mapping;    Mis-assembly;   

DOI  :  10.1186/s12864-016-2673-7

 received in 2015-12-17, accepted in 2016-04-22,  发布年份 2016

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Mariano et al. 2016