Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)
Top Cited Papers
Open Access
- 6 May 2014
- journal article
- research article
- Published by Oxford University Press (OUP) in Molecular Biology and Evolution
- Vol. 31 (8), 2223-2237
- https://doi.org/10.1093/molbev/msu154
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.Keywords
This publication has 50 references indexed in Scilit:
- IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depthBioinformatics, 2012
- PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic AnalysesMolecular Biology and Evolution, 2012
- Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major OrdersMolecular Biology and Evolution, 2011
- Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematicsNucleic Acids Research, 2010
- Revisiting the Insect Mitochondrial Molecular Clock: The Mid-Aegean Trench CalibrationMolecular Biology and Evolution, 2010
- Sequence-non-specific effects of RNA interference triggers and microRNA regulatorsNucleic Acids Research, 2009
- Temporal lags and overlap in the diversification of weevils and flowering plantsProceedings of the National Academy of Sciences of the United States of America, 2009
- A Comparative Analysis of Mitochondrial Genomes in Coleoptera (Arthropoda: Insecta) and Genome Descriptions of Six New BeetlesMolecular Biology and Evolution, 2008
- RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed modelsBioinformatics, 2006
- A Whole-Genome Assembly of DrosophilaScience, 2000