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

Diego César Batista Mariano,Tessália Diniz Luerce Saraiva,Carlos Augusto Gomes Leal,Flávia Rocha,Thiago De Jesus Sousa,Artur Silva,Alex Fiorini De Carvalho,Vasco Ariston Carvalho Azevedo,Fernanda Alves Dorella,Syed Shah Hassan,Flávia Aburjaile,Anne Cybelle Pinto,Felipe Luiz Pereira,Rommel Thiago Jucá Ramos,Henrique César Pereira Figueiredo,Debmalya Barh

doi:10.1186/s12864-016-2673-7

Diego César Batista Mariano, Tessália Diniz Luerce Saraiva + Show 14 more

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https://doi.org/10.1186/s12864-016-2673-7

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.

Highlights

Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis
The syntenic comparison between Corynebacterium pseudotuberculosis strain 1002 (Cp1002A) and Corynebacterium pseudotuberculosis strain 1002 (Cp1002B) (Fig. 3) shows a genetic inversion that occurs between two regions encoding ribosomal RNA
CP012837) was performed through a de novo strategy validated by experimental evidence (WGM), while the older assembly was performed by reference strategy

Summary

Introduction

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. Cp can be classified into two biovars: equi and ovis. The Cp31 strain that was originally sequenced using the SOLiD v3 platform and mate-pair library [9], was re-sequenced using Ion PGM platform [15]. This new sequencing discovered a new ~91 Kbp fragment in the Cp31 genome that is not present in NCBI. There are possibilities that some of the available Cp genomes in NCBI may be incomplete and warns resequencing, reassembly, and minimization or closing gaps

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