Abstract

Mitochondrial DNA (mtDNA) have long been used as a tool for genetic analyses, with most studies relying on sequence data from only one or two protein-coding regions, generally amounting to <2,000 base pairs of sequence data. The development of next-generation sequencing methods over the last decade has enabled the generation of large amounts of sequence data for an increasingly lower cost per base. These methods typically target nuclear DNA, but because of mtDNA’s abundance in most eukaryotic cells, mitochondrial regions are often sequenced as well. When indirect, or “off-target” mtDNA is obtained, it is often referred to as by-catch, implying that its inclusion in sequencing output was not the intention of the sequencing experiment. Because next-generation sequencing methods generate so many sequences per run (millions), by-catch regions can amount to substantial numbers of sequences and thus might prove useful. Indeed, many researchers now value these by-catch regions, particularly because they often allow the characterization of entire mitochondrial genomes (mitogenomes). It is possible to scale this up to simultaneously characterize mitogenomes of entire genera at a time. In this paper, sequence data from a related project was used to simultaneously identify, assemble, and annotate mitogenomes from an entire genus of boid snakes from the Caribbean (genus Chilabothrus). To date, no other study has attempted this for boas. Using millions of sequence reads generated from a targeted-capture sequencing project to search for mitochondrial by-catch, mitogenomes were assembled by comparison to known mitogenomes from GenBank. Then, mitogenomes were aligned and annotated to identify and label different gene regions. Finally, a series of protein-coding molecular phylogenies of the entire genus were generated using Bayesian and Maximum Likelihood methods. This study illustrates the feasibility of using sequencing by-catch to simultaneously assemble and annotate mitogenomes from large taxonomic groups, including an entire genus of snakes.

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