Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake

Product Type: Journal Article

Year: 2012

Author(s): Castoe, T.A., A.W. Poole, A.P. Koning, K.L. Jones, D.F. Tomback, S.J. Oyler-McCance, J.A. Fike, J.W. Streicher, E.N. Smith, and D.D. Pollock

Suggested Citation:
Castoe, T.A., A.W. Poole, A.P. Koning, K.L. Jones, D.F. Tomback, S.J. Oyler-McCance, J.A. Fike, 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): 1-10.

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...