The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains.
The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains.
复制标题
高通量测序和目标富集对烧焦的考古植物遗骸的功效。
DOI：
10.1038/srep37347
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发表时间：
2016
影响因子：
4.6
通讯作者：
Nistelberger HM
中科院分区：
文献类型：
--
作者：
Nistelberger HM
大多数考古植物材料以烧焦的状态保存。从这些遗骸中获得可靠的古代DNA数据面临着挑战，因为核苷酸损伤率高，DNA片段长度短，内源性DNA含量低以及现代污染的可能性。有人建议，高通量测序（HTS）技术与DNA富集技术相结合，可以克服这些限制。在这里，我们报告的结果HTS和目标富集四个重要的考古作物（大麦，葡萄，玉米和水稻）在三个不同的实验室进行，目前最大的HTS评估烧焦的考古植物标本。我们的数据的严格分析-排除假阳性，由于背景污染或不正确的索引分配-表明缺乏内源性DNA在几乎所有的样品，除了一个轻微烧焦的玉米棒。即使目标富集，该样本也未能产生解决考古学和生物学基本问题所需的足够数据。我们进一步重新分析了烧焦植物材料的现有数据集的一部分，发现所有所谓的内源性DNA序列都可能是假的。我们认为这些技术不适合用于烧焦的古植物，并敦促非常谨慎的解释HTS获得的数据时，这些仍然。
The majority of archaeological plant material is preserved in a charred state. Obtaining reliable ancient DNA data from these remains has presented challenges due to high rates of nucleotide damage, short DNA fragment lengths, low endogenous DNA content and the potential for modern contamination. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three different laboratories, presenting the largest HTS assessment of charred archaeobotanical specimens to date. Rigorous analysis of our data – excluding false-positives due to background contamination or incorrect index assignments – indicated a lack of endogenous DNA in nearly all samples, except for one lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely to be spurious. We suggest these technologies are not suitable for use with charred archaeobotanicals and urge great caution when interpreting data obtained by HTS of these remains.