Abstract
BackgroundTo date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species.ResultsWe selectively targeted 11,975 exons (~4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up to 20 barcoded individuals on a single array. Base coverage among specimens and within targets in each species library was uniform, and the performance of targets among independent exon captures was highly reproducible. There was no decrease in coverage among chipmunk species, which showed up to 1.5% sequence divergence in coding regions. We did observe a decline in capture performance of a subset of targets designed from a much more divergent ground squirrel genome (30 My), however, over 90% of the targets were also recovered. Final assemblies yielded over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs among species identified.ConclusionsOur study demonstrates the potential of a transcriptome-enabled, multiplexed, exon capture method to create thousands of informative markers for population genomic and phylogenetic studies in non-model species across the tree of life.
Highlights
To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources
Tamias alpinus transcriptome The T. alpinus multi-tissue cDNA library generated 30,233,530 raw sequence reads with a total length of 3.02 Gb (NCBI SRA ID: SRA053502)
There was a positive relationship between transcript length and the number of reads mapped, but we found no strong correlation between coverage and the length of contigs (Additional file 3: Figure S1)
Summary
Exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. Large-scale, multilocus data (i.e., hundreds to thousands of loci) combined with improved analytical tools for inferring gene trees, provides unprecedented opportunities for resolving species phylogenies [5]. Toward this end, a core challenge of population genomic and phylogenetic studies is obtaining a reliable set of orthologous loci from a sufficient number of individuals across populations or species spanning a range of divergences [6]. Whole genome data is not necessary to answer many research questions In this context, genome partitioning and targeted re-sequencing of a consistent subset of genomic regions will remain the most cost-effective and analytically straightforward approach for most evolutionary applications. The genomes of most organisms of ecological and evolutionary interest are yet to be sequenced, which has largely impeded the expansion of DNA capture across the tree of life
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