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.
Highlights
With the advent of high-throughput next-generation sequencing (NGS) technologies and their ability to generate large amounts of data suitable for genomic assembly, systematists are increasingly adopting such methods to reconstruct complete mitochondrial genomes to infer phylogenies across a diverse range of taxa
Mitogenomes have an intrinsic suitability for phylogenetic analysis due to their unambiguous orthology (Botero-Castro et al 2013), phylogenetic signal at diverse taxonomic ranks (Bernt et al 2013), broadly uniform rate of molecular evolution (Papadopoulou et al 2010), and uniparental inheritance consistent with bifurcating phylogenetic trees (Curole and Kocher 1999), even if phylogenetic analyses may be confounded by inconsistencies of the coalescent history near the species level (Funk and Omland 2003) and by lineage-specific compositional and rate heterogeneity at higher hierarchical levels (Sheffield et al 2009; Bernt et al 2013; Cameron 2014)
Following sequencing with an Illumina MiSeq, approximately 5% of the reads resembled mitochondrial sequences after BLAST filtering
Summary
With the advent of high-throughput next-generation sequencing (NGS) technologies and their ability to generate large amounts of data suitable for genomic assembly, systematists are increasingly adopting such methods to reconstruct complete mitochondrial genomes (mitogenomes) to infer phylogenies across a diverse range of taxa.
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