SREL Reprint #3202

Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake

Todd A. Castoe1, Alexander W. Poole1, A. P. Jason de Koning1, Kenneth L. Jones1, Diana F. Tomback2,
Sara J. Oyler-McCance3, Jennifer A. Fike3, Stacey L. Lance4, Jeffrey W. Streicher5, Eric N. Smith5,
and David D. Pollock1

1Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine,
Aurora, Colorado, USA
2Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, USA
3United States Geological Survey – Fort Collins Science Center, Fort Collins, Colorado, USA
4University of Georgia, Savannah River Ecology Laboratory, Aiken, South Carolina, USA
5Department of Biology and Amphibian and Reptile Diversity Research Center,
The University of Texas at Arlington, Arlington, Texas, USA

Abstract: Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct ‘‘Seq-to-SSR’’ approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark’s Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

SREL Reprint #3202

Castoe, T. A., A. W. Poole, A. P. J. de Koning, K. L. Jones, D. F. Tomback, S. J. Oyler-McCance, J. A. Fike, S. L. Lance, J. W. Streicher, E. N. Smith, and D. D. Pollock. 2012. Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake. PLos ONE 7(2): e30953.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).