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Home / Equine Research Bank / Microb Biotechnol / Tips and tricks for the assembly of a Corynebacterium pseudo...
Microbial biotechnology2012; 6(2); 150-156; doi: 10.1111/1751-7915.12006

Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer.

Abstract: New sequencing platforms have enabled rapid decoding of complete prokaryotic genomes at relatively low cost. The Ion Torrent platform is an example of these technologies, characterized by lower coverage, generating challenges for the genome assembly. One particular problem is the lack of genomes that enable reference-based assembly, such as the one used in the present study, Corynebacterium pseudotuberculosis biovar equi, which causes high economic losses in the US equine industry. The quality treatment strategy incorporated into the assembly pipeline enabled a 16-fold greater use of the sequencing data obtained compared with traditional quality filter approaches. Data preprocessing prior to the de novo assembly enabled the use of known methodologies in the next-generation sequencing data assembly. Moreover, manual curation was proved to be essential for ensuring a quality assembly, which was validated by comparative genomics with other species of the genus Corynebacterium. The present study presents a modus operandi that enables a greater and better use of data obtained from semiconductor sequencing for obtaining the complete genome from a prokaryotic microorganism, C. pseudotuberculosis, which is not a traditional biological model such as Escherichia coli.
© 2012 The Authors. Published by Society for Applied Microbiology and Blackwell Publishing Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Publication Date: 2012-12-02 PubMed ID: 23199210PubMed Central: PMC3917457DOI: 10.1111/1751-7915.12006Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research focuses on the process and techniques used by scientists for assembling the genome of a bacterium, Corynebacterium pseudotuberculosis biovar equi, using next-generation sequencing technology, specifically the Ion Torrent platform.

Assembly of a Bacterial Genome

  • The study begins by acknowledging the importance of new sequencing platforms like the Ion Torrent, which have allowed for the decoding of complete prokaryotic genomes at a relatively low cost.
  • One challenge with this technology is lower sequencing coverage, making genome assembly more difficult, especially for organisms with genome sequences not already thoroughly available for reference-based assembly.
  • In this case, the team addressed the genome sequencing of Corynebacterium pseudotuberculosis biovar equi, a bacterium that causes harm and economic loss to the US equine industry.

Quality Treatment Strategy and Assembly Pipeline

  • The strategy used in this research allowed for a 16-fold increase in the usage of sequencing data, compared to the traditional quality filter approaches.
  • In the assembly pipeline, data pre-processing was carried out before the de novo assembly, which is the assembly of a genome from scratch without using any reference genome.
  • This step was crucial as this allowed for the application of known methodologies in the next-generation sequencing data assembly.

Manual Curation and Genome Validation

  • Manual curation emerged as an invaluable part of ensuring the quality of the assembly. This involves reviewing and correcting the automatic outputs of a genome assembly.
  • The accuracy and quality of the assembly were then validated through a process of comparative genomics, whereby the genome of the studied organism was cross-examined against genomes of other Corynebacterium species.

Novel Modus Operandi

  • The study presents a unique workflow for effectively using data from semiconductor sequencing to obtain the complete genome of prokaryotic microbes like Corynebacterium pseudotuberculosis.
  • This method can be particularly useful when dealing with organisms that are not traditional biological models like E. coli, where the genome is well-documented.

Cite This Article

APA
Ramos RT, Carneiro AR, Soares Sde C, dos Santos AR, Almeida S, Guimarães L, Figueira F, Barbosa E, Tauch A, Azevedo V, Silva A. (2012). Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. Microb Biotechnol, 6(2), 150-156. https://doi.org/10.1111/1751-7915.12006

Publication

Microbial biotechnology
ISSN: 1751-7915
NlmUniqueID: 101316335
Country: United States
Language: English
Volume: 6
Issue: 2
Pages: 150-156

Researcher Affiliations

Ramos, Rommel Thiago Jucá
  • Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil.
Carneiro, Adriana Ribeiro
    Soares, Siomar de Castro
      dos Santos, Anderson Rodrigues
        Almeida, Sintia
          Guimarães, Luis
            Figueira, Flávia
              Barbosa, Eudes
                Tauch, Andreas
                  Azevedo, Vasco
                    Silva, Artur

                      MeSH Terms

                      • Animals
                      • Computational Biology / methods
                      • Corynebacterium Infections / microbiology
                      • Corynebacterium Infections / veterinary
                      • Corynebacterium pseudotuberculosis / genetics
                      • Corynebacterium pseudotuberculosis / isolation & purification
                      • DNA, Bacterial / analysis
                      • Electrochemical Techniques / instrumentation
                      • Electrochemical Techniques / methods
                      • Equipment Design
                      • Genome, Bacterial / genetics
                      • Genomics / methods
                      • Horse Diseases / microbiology
                      • Horses
                      • Semiconductors
                      • Sequence Analysis, DNA / instrumentation
                      • Sequence Analysis, DNA / methods
                      • Software

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                      Citations

                      This article has been cited 11 times.
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                      3. Almeida S, Sousa C, Abreu V, Diniz C, Dorneles EM, Lage AP, Barh D, Azevedo V. Exploration of Nitrate Reductase Metabolic Pathway in Corynebacterium pseudotuberculosis.. Int J Genomics 2017;2017:9481756.
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                      4. Baraúna RA, Ramos RTJ, Veras AAO, de Sá PHCG, Guimarães LC, das Graças DA, Carneiro AR, Edman JM, Spier SJ, Azevedo V, Silva A. Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection.. Stand Genomic Sci 2017;12:16.
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