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

    Authors

    T. A. Castoe; A. W. Poole; W. J. Gu; A. P. J. de Koning; J. M. Daza; E. N. Smith;D. D. Pollock

    Comments

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    Abbreviated Journal Title

    Mol. Ecol. Resour.

    Keywords

    high-throughput marker identification; next-generation sequencing; simple sequence repeats; snake genomics; Viperidae; EUKARYOTIC GENOMES; MARKERS; Biochemistry & Molecular Biology; Ecology; Evolutionary Biology

    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 similar to 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.

    Journal Title

    Molecular Ecology Resources

    Volume

    10

    Issue/Number

    2

    Publication Date

    1-1-2010

    Document Type

    Article

    Language

    English

    First Page

    341

    Last Page

    347

    WOS Identifier

    WOS:000274325400012

    ISSN

    1755-098X

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