title: Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea).
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.
authors.affiliation: Department of Life Sciences, Natural History Museum, London, United KingdomSchool of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United Kingdom c.gillett@uea.ac.uk a.vogler@nhm.ac.uk.
authors.forename: Conrad P D T
authors.initials: CP
authors.lastname: Gillett
authors.affiliation: Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Genetics, Evolution and Environment, University College London, London, United Kingdom.
authors.forename: Alex
authors.initials: A
authors.lastname: Crampton-Platt
authors.affiliation: Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom.
authors.forename: Martijn J T N
authors.initials: MJ
authors.lastname: Timmermans
authors.affiliation: The Natural History Museum, University Museum of Bergen, Bergen, Norway.
authors.forename: Bjarte H
authors.initials: BH
authors.lastname: Jordal
authors.affiliation: School of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United KingdomIsland Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, La Laguna, Tenerife, Canary Islands, Spain.
authors.forename: Brent C
authors.initials: BC
authors.lastname: Emerson
authors.affiliation: Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom c.gillett@uea.ac.uk a.vogler@nhm.ac.uk.
authors.forename: Alfried P
authors.initials: AP
authors.lastname: Vogler
mesh_terms: D000818:Animals; D004247:DNA / Q000032:analysis; D019143:Evolution, Molecular; D049750:Genome, Insect; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D048889:Weevils / Q000145:classification* / Q000235:genetics
chemical_list: D004247:DNA
keywords: MiSeq; genomics; mitochondria; next-generation sequencing; phylogenetics; wood-boring