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Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

Maddock, ST; Briscoe, AG; Wilkinson, M; Waeschenbach, A; San Mauro, D; Day, JJ; Littlewood, DT; ... Gower, DJ; + view all (2016) Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. PLoS One , 11 (6) , Article e0156757. 10.1371/journal.pone.0156757. Green open access

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Abstract

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.

Type: Article
Title: Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0156757
Publisher version: http://dx.doi.org/10.1371/journal.pone.0156757
Language: English
Additional information: © 2016 Maddock et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/1497472
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