High-throughput sequencing of complete mitochondrial genomes
Briscoe, A.G.; Hopkins, K.P.; Waeschenbach, A. (2016). High-throughput sequencing of complete mitochondrial genomes, in: Bourlat, S.J. (Ed.) Marine genomics: methods and protocols. Methods in Molecular Biology, 1452: pp. 45-64. https://dx.doi.org/10.1007/978-1-4939-3774-5_3
In: Bourlat, S.J. (Ed.) (2016). Marine genomics: methods and protocols. Methods in Molecular Biology, 1452. Humana Press/Springer Science+Business Media, Inc: New York. ISBN 978-1-4939-3772-1. 253 pp. https://dx.doi.org/10.1007/978-1-4939-3774-5, more
In: Methods in Molecular Biology. Humana Press. ISSN 1064-3745, more
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| Author keywords |
Illumina; MiSeq; Long-range PCR; Shotgun sequencing; Mitogenomics; Multiplexing |
| Authors | | Top |
- Briscoe, A.G.
- Hopkins, K.P.
- Waeschenbach, A.
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| 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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