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Open Access Highly Accessed Methodology article

Exome-wide DNA capture and next generation sequencing in domestic and wild species

Ted Cosart123*, Albano Beja-Pereira3*, Shanyuan Chen3, Sarah B Ng4, Jay Shendure4 and Gordon Luikart35

Author Affiliations

1 Department of Computer Science, University of Montana, Missoula, MT, USA

2 Montana-Ecology of Infectious Diseases Program, The University of Montana, Missoula, MT, USA

3 Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade do Porto, Rua Padre Armando Quintas 7, Campus Agrário de Vairão, 4485-661 Vairão, Portugal

4 Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA

5 Flathead Lake Biological Station and Division of Biological Sciences, University of Montana, Polson, MT 59860, USA

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BMC Genomics 2011, 12:347  doi:10.1186/1471-2164-12-347

Published: 5 July 2011

Abstract

Background

Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.

We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus) to capture (enrich for), and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits.

Results

We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes.

Conclusions

This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.