Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea)

Gillett, Conrad P. D. T., Crampton-Platt, Alex, Timmermans, Martijn J. T. N., Jordal, Bjarte H., Emerson, Brent C. and Vogler, Alfried P. (2014) Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Molecular Biology and Evolution, 31 (8). pp. 2223-2237. ISSN 0737-4038

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Abstract

Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based “bait” sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.

Item Type:	Article
Additional Information:	© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords:	next-generation sequencing,genomics,miseq,mitochondria,phylogenetics,wood-boring
Faculty \ School:	Faculty of Science Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Organisms and the Environment
Depositing User:	Pure Connector
Date Deposited:	25 Jul 2014 14:54
Last Modified:	04 Jul 2023 10:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/49747
DOI:	10.1093/molbev/msu154

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