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Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence

Authors

  • TODD A. CASTOE,

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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  • ALEXANDER W. POOLE,

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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  • WANJUN GU,

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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    • §

      Present address: Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing 210096, China.

  • A. P. JASON de KONING,

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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  • JUAN M. DAZA,

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
    2. Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA
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  • ERIC N. SMITH,

    1. Department of Biology & Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX 76019, USA
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  • DAVID D. POLLOCK

    1. Consortium for Comparative Genomics, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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  • The first two authors contributed equally.

David D. Pollock, Fax: +1 303 724 3215; E-mail: david.pollock@ucdenver.edu

Abstract

Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next-generation sequencing platform to sample randomly ∼27 Mbp (128 773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14 612 microsatellite loci identified in total, 4564 of which had flanking sequences suitable for polymerase chain reaction primer design. The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species.

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