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High-Throughput Sequencing of Complete Mitochondrial Genomes

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Marine Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1452))

Abstract

Next-generation sequencing has revolutionized mitogenomics, turning a cottage industry into a high throughput process. This chapter outlines methodologies used to sequence, assemble, and annotate mitogenomes of non-model organisms using Illumina sequencing technology, utilizing either long-range PCR amplicons or gDNA as starting template. Instructions are given on how to extract DNA, conduct long-range PCR amplifications, generate short Sanger barcode tag sequences, prepare equimolar sample pools, construct and assess quality library preparations, assemble Illumina reads using either seeded reference mapping or de novo assembly, and annotate mitogenomes in the absence of an automated pipeline. Notes and recommendations, derived from our own experience, are given throughout this chapter.

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Acknowledgments

This work was partly funded by an NHM postdoctoral position to AB through the NHM Disease Initiative. The authors thank Tim Littlewood and Bonnie Webster for constructive comments on an earlier draft.

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Authors and Affiliations

  1. Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK

    Andrew George Briscoe, Kevin Peter Hopkins & Andrea Waeschenbach

Authors
  1. Andrew George Briscoe
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  2. Kevin Peter Hopkins
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  3. Andrea Waeschenbach
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Corresponding author

Correspondence to Andrew George Briscoe .

Editor information

Editors and Affiliations

  1. Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden

    Sarah J. Bourlat

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Briscoe, A.G., Hopkins, K.P., Waeschenbach, A. (2016). High-Throughput Sequencing of Complete Mitochondrial Genomes. In: Bourlat, S. (eds) Marine Genomics. Methods in Molecular Biology, vol 1452. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3774-5_3

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  • DOI: https://doi.org/10.1007/978-1-4939-3774-5_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3772-1

  • Online ISBN: 978-1-4939-3774-5

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