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

ABSTRACT:

Background

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.

Results

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 librar

SUBMITTER: Bi K 

PROVIDER: S-EPMC3472323 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature