Mariano Diego César Batista, Sousa Thiago de Jesus, Pereira Felipe Luiz, Aburjaile Flávia, Barh Debmalya, Rocha Flávia, Pinto Anne Cybelle, Hassan Syed Shah, Saraiva Tessália Diniz Luerce, Dorella Fernanda Alves, de Carvalho Alex Fiorini, Leal Carlos Augusto Gomes, Figueiredo Henrique César Pereira, Silva Artur, Ramos Rommel Thiago Jucá, Azevedo Vasco Ariston Carvalho
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.
BMC Genomics. 2016 Apr 30;17:315. doi: 10.1186/s12864-016-2673-7.
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.
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.
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.
研究已在伪结核棒状杆菌的基因组中检测到错误组装。由于新一代测序平台的发展，这些新发现成为可能，新一代测序平台提供了准确且成本降低的测序。此外，高精度基因组图谱构建技术的改进，例如全基因组图谱绘制（WGM）（OpGen公司），使得能够进行高分辨率组装，从而检测到大的重排。
在这项工作中，我们展示了伪结核棒状杆菌1002菌株（Cp1002）的重测序。Cp1002是该物种在巴西测序的首个菌株，其基因组已被用作干酪性淋巴结炎疾病多项计算机模拟研究的模型。使用Ion PGM平台和片段文库（200 bp试剂盒）进行测序。使用KpnI酶通过WGM技术构建了限制性图谱。在以WGM作为支架进行新的组装过程后，我们检测到一个大小超过基因组一半的大倒位。使用BLAST和NR数据库进行的特定分析表明，倒位发生在两个同源RNA核糖体区域之间。
总之，WGM显示的结果可用于检测组装中的错配，提供高分辨率的基因组图谱，并允许进行更准确和完整的组装。伪结核棒状杆菌的新组装序列已存入GenBank，登录号为CP012837。
