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

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Maddock, Simon T. and Briscoe, Andrew G. and Wilkinson, Mark and Waeschenbach, Andrea and San Mauro, Diego and Day, Julia J. and Littlewood, D. Tim J. and Foster, Peter G. and Nussbaum, Ronald A. and Gower, David J. (2016) Next-Generation Mitogenomics:A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny. Plos One . pp. 1-15. ISSN ESSN: 1932-6203

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Official URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156757



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.


Item Type:Article
Uncontrolled Keywords:Mitogenome; Caecilian Amphibian; Phylogeny; Seychelles
Subjects:Medical sciences > Biology > Amphibians
Medical sciences > Biology > Genetics
ID Code:46178
Deposited On:24 Jan 2018 12:18
Last Modified:10 Dec 2018 15:25

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