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Updated: May 19, 2026
11:52
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate
Ke Bi1, Dan Vanderpool, Sonal Singhal
1Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160, USA. kebi@berkeley.edu
BMC Genomics
|August 21, 2012
Summary
This study introduces a novel exon capture method using de novo transcriptome assemblies for non-model organisms. This approach successfully generated thousands of genetic markers for population genomics and phylogenetic studies in chipmunks.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Exon capture typically requires fully sequenced genomes, limiting its use in species lacking high-quality genomic resources.
- A novel strategy was developed for array-based exon capture in chipmunks (Tamias) utilizing de novo transcriptome assemblies.
- The method's performance was assessed across four chipmunk species.
Purpose of the Study:
- To develop and evaluate a novel exon capture strategy for non-model organisms.
- To enable population genomic and phylogenetic studies in lineages without existing genomic resources.
- To create thousands of informative genetic markers for evolutionary research.
Main Methods:
- Designed custom capture arrays targeting 11,975 exons (~4 Mb) based on de novo transcriptome assemblies.
- Enriched over 99% of targets across all libraries with consistent read alignment percentages (24.4-29.1%).
- Successfully multiplexed up to 20 barcoded individuals on a single array, demonstrating reproducibility and uniform base coverage.
Main Results:
- High target enrichment (>99%) and consistent read alignment percentages across chipmunk species.
- Uniform base coverage and reproducible performance among independent exon captures, even with up to 1.5% sequence divergence.
- Over 90% target recovery even with probes designed from a highly divergent ground squirrel genome (30 Mya).
- Generated over ten thousand orthologous loci (~3.6 Mb) with thousands of fixed and polymorphic SNPs identified.
Conclusions:
- Demonstrates the efficacy of a transcriptome-enabled, multiplexed exon capture method for non-model species.
- Provides a powerful tool for generating thousands of informative markers for population genomics and phylogenetic studies.
- Expands the application of exon capture to diverse lineages lacking high-quality genomic resources across the tree of life.
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