Open Access Highly Accessed Open Badges Methodology article

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

Ke Bi1*, Dan Vanderpool2, Sonal Singhal13, Tyler Linderoth13, Craig Moritz13 and Jeffrey M Good2

Author Affiliations

1 Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA

2 Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA

3 Department of Integrative Biology, University of California, Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA, 94720-3140, USA

For all author emails, please log on.

BMC Genomics 2012, 13:403  doi:10.1186/1471-2164-13-403

Published: 17 August 2012



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. 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.


We 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.


Our 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.

Microarray-based exon capture; Phylogenetics; Population genomics; SNP identification; Tamias; Target enrichment