Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data
Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data
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DOI：
10.2144/000113086
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发表时间：
2009-03-01
期刊：
影响因子：
2.7
通讯作者：
Bunce, Michael
中科院分区：
文献类型：
--
作者：
Allentoft, Morten E.;Schuster, Stephan C.;Bunce, Michael
由于化石记录中的核DNA数量很少，以及灭绝物种缺乏特征性的核标记，因此在古DNA（aDNA）领域很少研究微卫星遗传变异。454测序平台提供了一种新的高通量技术，每次运行能够产生高达1千兆碱基的短（200-400-bp）读取长度。454个数据是从一种已灭绝的新西兰恐鸟（鸟类：恐龙形目）的化石骨骼中产生的。我们确定了许多短串联重复序列（STR）基序，并在这里提出了一个多态性微卫星（Moa_MS2）的成功分离和表征。引物设计侧翼这个位点扩增所有三个恐鸟物种在这里测试。所提出的方法被证明是一种快速有效的方法，确定微卫星标记在古老的DNA模板，并依赖于生物分子的保存，有可能使高分辨率的种群遗传学研究的灭绝类群。作为454平台及其竞争者（例如，随着SOLEXA和SOLO平台）的增加，这种方法在确定灭绝（和现存）生物体中的微卫星方面将变得越来越强大，并将为研究过去的生物多样性和灭绝过程提供新的机会。
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 SOLO 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.