Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data

TY - JOUR

T1 - Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data

AU - Allentoft, Morten Erik

AU - Schuster, Stephan C.

AU - Holdaway, Richard N.

AU - Hale, Marie L.

AU - McLay, Emma

AU - Oskam, Charlotte L.

AU - Gilbert, M Thomas P

AU - Spencer, Peter

AU - Willerslev, Eske

AU - Bunce, Michael

N1 - Keywords: Algorithms; Animals; Base Sequence; Chromosome Mapping; Extinction, Biological; Fossils; Microsatellite Repeats; Molecular Sequence Data; Palaeognathae; Reproducibility of Results; Sensitivity and Specificity; Sequence Analysis, DNA; Species Specificity

PY - 2009

Y1 - 2009

N2 - Genetic variation in microsatellites is rarely examined in the field of ancient DNA (aDNA) due to the low quantity of nuclear DNA in the fossil record together with the lack of characterized nuclear markers in extinct species. 454 sequencing platforms provide a new high-throughput technology capable of generating up to 1 gigabases per run as short (200-400-bp) read lengths. 454 data were generated from the fossil bone of an extinct New Zealand moa (Aves: Dinornithiformes). We identified numerous short tandem repeat (STR) motifs, and here present the successful isolation and characterization of one polymorphic microsatellite (Moa_MS2). Primers designed to flank this locus amplified all three moa species tested here. The presented method proved to be a fast and efficient way of identifying microsatellite markers in ancient DNA templates and, depending on biomolecule preservation, has the potential of enabling high-resolution population genetic studies of extinct taxa. As sequence read lengths of the 454 platforms and its competitors (e.g., the SOLEXA and SOLiD platforms) increase, this approach will become increasingly powerful in identifying microsatellites in extinct (and extant) organisms, and will afford new opportunities to study past biodiversity and extinction processes.

AB - Genetic variation in microsatellites is rarely examined in the field of ancient DNA (aDNA) due to the low quantity of nuclear DNA in the fossil record together with the lack of characterized nuclear markers in extinct species. 454 sequencing platforms provide a new high-throughput technology capable of generating up to 1 gigabases per run as short (200-400-bp) read lengths. 454 data were generated from the fossil bone of an extinct New Zealand moa (Aves: Dinornithiformes). We identified numerous short tandem repeat (STR) motifs, and here present the successful isolation and characterization of one polymorphic microsatellite (Moa_MS2). Primers designed to flank this locus amplified all three moa species tested here. The presented method proved to be a fast and efficient way of identifying microsatellite markers in ancient DNA templates and, depending on biomolecule preservation, has the potential of enabling high-resolution population genetic studies of extinct taxa. As sequence read lengths of the 454 platforms and its competitors (e.g., the SOLEXA and SOLiD platforms) increase, this approach will become increasingly powerful in identifying microsatellites in extinct (and extant) organisms, and will afford new opportunities to study past biodiversity and extinction processes.

U2 - 10.2144/000113086

DO - 10.2144/000113086

M3 - Journal article

C2 - 19317662

SN - 0736-6205

VL - 46

SP - 195

EP - 200

JO - BioTechniques

JF - BioTechniques

IS - 3

ER -