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Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets

  • María de ToroEmail author
  • Val F. Lanza
  • Luis Vielva
  • Santiago Redondo-Salvo
  • Fernando de la Cruz
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2075)

Abstract

Mobile Genetic Elements (MGE) play essential roles in adaptive bacterial evolution, facilitating genetic exchange for extrachromosomal DNA, especially antibiotic resistance genes and virulence factors. For this reason, high-throughput next-generation sequencing of bacteria is of great relevance, especially for clinical pathogenic bacteria. Accurate identification of MGE from whole-genome sequencing (WGS) datasets is one of the major challenges, still hindered by methodological limitations and high sequencing costs.

This chapter encompasses the protocol used for plasmid reconstruction by applying the PLACNETw methodology, from raw reads to assembled plasmids and chromosome. PLACNETw is a graphical user-friendly interface to visualize and reconstruct MGE from short-read WGS datasets. No bioinformatic background or sophisticated computational resources are required and high precision and sensitivity are achieved.

Key words

Mobile genetic elements Whole genome sequencing Plasmids ICEs 

Supplementary material

Video

(MP4 558,193 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • María de Toro
    • 1
    Email author
  • Val F. Lanza
    • 2
    • 3
    • 4
  • Luis Vielva
    • 5
  • Santiago Redondo-Salvo
    • 6
  • Fernando de la Cruz
    • 6
  1. 1.Plataforma de Genómica y BioinformáticaCentro de Investigación Biomédica de La Rioja (CIBIR) - Fundación Rioja Salud (FRS)LogroñoSpain
  2. 2.Department of MicrobiologyRamón y Cajal University Hospital (IRYCIS)MadridSpain
  3. 3.CIBER in Epidemiology and Public Health, (CIBERESP)MadridSpain
  4. 4.Bioinformatics UnitRamón y Cajal Universitary Hospital (IRYCIS)MadridSpain
  5. 5.Departamento de Ingeniería de ComunicacionesUniversidad de CantabriaSantanderSpain
  6. 6.Instituto de Biomedicina y Biotecnología de CantabriaUniversidad de Cantabria-CSICSantanderSpain

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