title: Optimized construction of microsatellite-enriched libraries.
abstract: The construction of microsatellite-enriched libraries is an indispensable tool to search for molecular markers as complete genome sequences are still not available for the majority of species of interest. Numerous protocols are available in the literature for the construction of these libraries; however, sometimes their low efficiency or lack of optimization in the protocols can restrict their efficacy. We have designed and tested various adapters and ligation methods; we also tested oligo-repeat combinations and hybridization temperatures, and created libraries with this new protocol for four organisms: Ipomoea batatas (L.) Lam, Chionanthus retusus Lindley & Paxton, Rotylenchulus reniformis Linford & Olivera and Puccinia kuehnii W. Krüger. The number of microsatellites detected for these species ranged from 2494 to 3919 per Mb of nonredundant sequence, that was 0.86 and 1.53 microsatellites per contig, with 37-66% of di-nucleotide motifs and 21-49% of tri- to octa-nucleotide repeats combined. A simplified protocol is provided for the successful generation of SSR-enriched libraries.
authors.affiliation: Department of Pharmacognosy, School of Pharmacy, National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, PO Box 1848, University of Mississippi, MS, USA USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, USA USDA-ARS, 12990 US Highway 441 N, Canal Point, FL, USA USDA-ARS-NPURU, PO Box 1848, University of Mississippi, MS, USA.
authors.forename: Natascha
authors.initials: N
authors.lastname: Techen
authors.forename: Renée S
authors.initials: RS
authors.lastname: Arias
authors.forename: Neil C
authors.initials: NC
authors.lastname: Glynn
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Pan
authors.forename: Ikhlas A
authors.initials: IA
authors.lastname: Khan
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler