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

Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Siomar de Castro Soares, Anderson Rodrigues dos Santos, Sintia Almeida, Luis Guimarães, Flávia Figueira, Eudes Guilherme Vieria Barbosa, Andreas Tauch, Vasco Azevedo, Artur Silva

Research output: Contribution to journalJournal articleResearchpeer-review

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.
Original languageEnglish
JournalMicrobial Biotechnology
Volume6
Issue number2
Pages (from-to)150-6
ISSN1751-7907
DOIs
Publication statusPublished - 2013

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Corynebacterium pseudotuberculosis
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Biological Models
Nimodipine
Horses
Ions
Microorganisms
Escherichia coli
Decoding
Pipelines
Economics

Keywords

  • Animals
  • Computational Biology
  • Corynebacterium Infections
  • Corynebacterium pseudotuberculosis
  • DNA, Bacterial
  • Electrochemical Techniques
  • Equipment Design
  • Genome, Bacterial
  • Genomics
  • Horse Diseases
  • Horses
  • Semiconductors
  • Sequence Analysis, DNA
  • Software

Cite this

Ramos, R. T. J., Carneiro, A. R., Soares, S. D. C., dos Santos, A. R., Almeida, S., Guimarães, L., ... Silva, A. (2013). Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. Microbial Biotechnology, 6(2), 150-6. https://doi.org/10.1111/1751-7915.12006
Ramos, Rommel Thiago Jucá ; Carneiro, Adriana Ribeiro ; Soares, Siomar de Castro ; dos Santos, Anderson Rodrigues ; Almeida, Sintia ; Guimarães, Luis ; Figueira, Flávia ; Barbosa, Eudes Guilherme Vieria ; Tauch, Andreas ; Azevedo, Vasco ; Silva, Artur. / Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. In: Microbial Biotechnology. 2013 ; Vol. 6, No. 2. pp. 150-6.
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title = "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.",
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Ramos, RTJ, Carneiro, AR, Soares, SDC, dos Santos, AR, Almeida, S, Guimarães, L, Figueira, F, Barbosa, EGV, Tauch, A, Azevedo, V & Silva, A 2013, 'Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer', Microbial Biotechnology, vol. 6, no. 2, pp. 150-6. https://doi.org/10.1111/1751-7915.12006

Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer. / Ramos, Rommel Thiago Jucá; Carneiro, Adriana Ribeiro; Soares, Siomar de Castro; dos Santos, Anderson Rodrigues; Almeida, Sintia; Guimarães, Luis; Figueira, Flávia; Barbosa, Eudes Guilherme Vieria; Tauch, Andreas; Azevedo, Vasco; Silva, Artur.

In: Microbial Biotechnology, Vol. 6, No. 2, 2013, p. 150-6.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Tips and tricks for the assembly of a Corynebacterium pseudotuberculosis genome using a semiconductor sequencer

AU - Ramos, Rommel Thiago Jucá

AU - Carneiro, Adriana Ribeiro

AU - Soares, Siomar de Castro

AU - dos Santos, Anderson Rodrigues

AU - Almeida, Sintia

AU - Guimarães, Luis

AU - Figueira, Flávia

AU - Barbosa, Eudes Guilherme Vieria

AU - Tauch, Andreas

AU - Azevedo, Vasco

AU - Silva, Artur

N1 - © 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.

PY - 2013

Y1 - 2013

N2 - 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.

AB - 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.

KW - Animals

KW - Computational Biology

KW - Corynebacterium Infections

KW - Corynebacterium pseudotuberculosis

KW - DNA, Bacterial

KW - Electrochemical Techniques

KW - Equipment Design

KW - Genome, Bacterial

KW - Genomics

KW - Horse Diseases

KW - Horses

KW - Semiconductors

KW - Sequence Analysis, DNA

KW - Software

U2 - 10.1111/1751-7915.12006

DO - 10.1111/1751-7915.12006

M3 - Journal article

VL - 6

SP - 150

EP - 156

JO - Microbial Biotechnology

JF - Microbial Biotechnology

SN - 1751-7907

IS - 2

ER -