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

Morten Erik Allentoft; Stephan C. Schuster; Richard N. Holdaway; Marie L. Hale; Emma McLay; Charlotte L. Oskam; M Thomas P Gilbert; Peter Spencer; Eske Willerslev; Michael Bunce

doi:10.2144/000113086

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

Morten Erik Allentoft, Stephan C. Schuster, Richard N. Holdaway, Marie L. Hale, Emma McLay, Charlotte L. Oskam, M Thomas P Gilbert, Peter Spencer, Eske Willerslev, Michael Bunce

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

90 Citationer (Scopus)

Abstract

Udgivelsesdato: 2009-Mar

Originalsprog	Engelsk
Tidsskrift	BioTechniques
Vol/bind	46
Udgave nummer	3
Sider (fra-til)	195-200
Antal sider	5
ISSN	0736-6205
DOI	https://doi.org/10.2144/000113086
Status	Udgivet - 2009

Bibliografisk note

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

Adgang til dokumentet

10.2144/000113086

Citationsformater

@article{7515d5008d8711de8bc9000ea68e967b,

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

abstract = "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.",

author = "Allentoft, {Morten Erik} and Schuster, {Stephan C.} and Holdaway, {Richard N.} and Hale, {Marie L.} and Emma McLay and Oskam, {Charlotte L.} and Gilbert, {M Thomas P} and Peter Spencer and Eske Willerslev and Michael Bunce",

note = "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",

year = "2009",

doi = "10.2144/000113086",

language = "English",

volume = "46",

pages = "195--200",

journal = "BioTechniques",

issn = "0736-6205",

publisher = "Informa Healthcare",

number = "3",

}

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 -