A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions
A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions
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DOI：
10.1002/tax.581003
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发表时间：
2009-02-01
期刊：
影响因子：
3.4
通讯作者：
Clarkson, James J.
中科院分区：
文献类型：
--
作者：
Devey, Dion S.;Chase, Mark W.;Clarkson, James J.
质体微卫星是简单的单/二核苷酸重复序列，其可引起体外Taq聚合酶错误，导致降低电泳图的清晰度和可靠性的“断续”峰。作为一个有效的和自动化的条形码协议需要高质量的原始数据，本文研究的适用性的质粒基因组的psbA-trnH和atpF-H区域的自动条形码的目的。从物种对和三胞胎的92个个体进行扩增。其中，59%的atpF-H物种样品和36%的psbA-trnH物种样品显示出微卫星诱导的电泳碱基识别错误的证据。人为干预的下游必要性使得这些非编码区对于条形码目的而言是次优的。
Plastid microsatellites are simple mono/dinucleotide repeats that can cause in-vitro taq polymerase errors leading to 'stutter' peaks that reduce the clarity and reliability of electropherograms. As an efficient and automated barcoding protocol requires high-quality raw data, this paper investigates the suitability of the psbA-trnH and atpF-H regions of the plastid genome for automated barcoding purposes. Amplification of 92 individuals from species pairs and triplets was undertaken. Of these, 59% of atpF-H species samples and 36% of psbA-trnH species samples showed evidence of rnicrosatellite-induced errors in electropherogram base calling. The downstream necessity of human intervention renders these non-coding regions sub-optimal for barcoding purposes.