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Mitochondrial DNA
The Journal of DNA Mapping, Sequencing, and Analysis
Volume 26, 2015 - Issue 3
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Research Article

Blood from a turnip: tissue origin of low-coverage shotgun sequencing libraries affects recovery of mitogenome sequences

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Pages 384-388 | Received 30 May 2013, Accepted 30 Aug 2013, Published online: 14 Oct 2013
 

abstract

Next generation sequencing methods allow rapid, economical accumulation of data that have many applications, even at relatively low levels of genome coverage. However, the utility of shotgun sequencing data sets for specific goals may vary depending on the biological nature of the samples sequenced. We show that the ability to assemble mitogenomes from three avian samples of two different tissue types varies widely. In particular, data with coverage typical of microsatellite development efforts (∼1×) from DNA extracted from avian blood failed to cover even 50% of the mitogenome, relative to at least 500-fold coverage from muscle-derived data. Researchers should consider possible applications of their data and select the tissue source for their work accordingly. Practitioners analyzing low-coverage shotgun sequencing data (including for microsatellite locus development) should consider the potential benefits of mitogenome assembly, including internal barcode verification of species identity, mitochondrial primer development, and phylogenetics.

Acknowledgements

We thank M. J. Dufort, H. Vázquez-Miranda, and M. T. Wells for comments on the manuscript. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Declaration of interest

The authors declare no conflicts of interests. The authors alone are responsible for the content and writing of this article.

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