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Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms

Damien D. Hinsinger
  • Institut de Systématique, Évolution, Biodiversité ISYEB, UMR 7205 CNRS, MNHN, UPMC, EPHE Muséum national d’Histoire naturelle, Sorbonne Universités. 57 rue Cuvier, CP30, 75005 Paris, France
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/ Regis Debruyne
  • Outils et Méthodes de la Systématique Intégrative, UMS 2700, MNHN, CNRS, Muséum national d’Histoire naturelle, Sorbonne Universités. 57 rue Cuvier, CP26, 75005 Paris, France
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/ Maeva Thomas
  • Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208), Sorbonne Universités, Muséum national d’Histoire naturelle, Université Pierre et Marie Curie, Université de Caen Basse-Normandie, CNRS, IRD, 57 rue Cuvier, CP26, 75005 Paris, France
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/ Gaël P. J. Denys
  • Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208), Sorbonne Universités, Muséum national d’Histoire naturelle, Université Pierre et Marie Curie, Université de Caen Basse-Normandie, CNRS, IRD, 57 rue Cuvier, CP26, 75005 Paris, France
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/ Marion Mennesson
  • Unité Biologie des organismes et écosystèmes aquatiques (BOREA, UMR 7208), Sorbonne Universités, Muséum national d’Histoire naturelle, Université Pierre et Marie Curie, Université de Caen Basse-Normandie, CNRS, IRD, 57 rue Cuvier, CP26, 75005 Paris, France
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/ Jose Utage
  • Outils et Méthodes de la Systématique Intégrative, UMS 2700, MNHN, CNRS, Muséum national d’Histoire naturelle, Sorbonne Universités. 57 rue Cuvier, CP26, 75005 Paris, France
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/ Agnes Dettai
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  • Institut de Systématique, Évolution, Biodiversité ISYEB, UMR 7205 CNRS, MNHN, UPMC, EPHE Muséum national d’Histoire naturelle, Sorbonne Universités. 57 rue Cuvier, CP30, 75005 Paris, France
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Published Online: 2015-11-26 | DOI: https://doi.org/10.1515/dna-2015-0019


The adoption of Next-Generation Sequencing (NGS) by the field of DNA barcoding of Metazoa has been hindered by the fit between the classical COI barcode and the Sanger-based sequencing method. Here we describe a framework for the sequencing and multiplexing of mitogenomes on NGS platforms that implements (I) a universal long-range PCR-based amplification technique, (II) a two-level multiplexing approach (i.e. divergence-based and specific tag indexing), and (III) a dedicated demultiplexing and assembling script from an Ion Torrent sequencing platform. We provide a case study of mitogenomes obtained for two vouchered individuals of daces Leuciscus burdigalensis and L. oxyrrhis and show that this workflow enables to recover over 100 mitogenomes per sequencing chip on a PGM sequencer, bringing the individual cost down below 7,50€ per mitogenome (as of current 2015 sequencing costs). The use of several kilobases for identification purposes, as involved in the improved DNA-barcode we propose, stress the need for data reliability, especially through metadata. Based on both scientific and economic considerations, this framework presents a relevant approach for multiplexing samples, adaptable on any desktop NGS platform. It enables to extend from the prevalent barcoding approach by shifting from the single COI to complete mitogenome sequencing

This article offers supplementary material which is provided at the end of the article.

Keywords: DNA barcoding; mitogenome assembly; Next- Generation Sequencing; sample multiplexing; sequence post-processing


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About the article

Received: 2015-03-31

Accepted: 2015-09-08

Published Online: 2015-11-26

Published in Print: 2015-01-01

Citation Information: DNA Barcodes, Volume 3, Issue 1, Pages 170–186, ISSN (Online) 2299-1077, DOI: https://doi.org/10.1515/dna-2015-0019.

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