Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.
Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.
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DOI：
10.1371/journal.pone.0024161
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Lalueza-Fox C
中科院分区：
文献类型：
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作者：
García-Garcerà M;Gigli E;Sanchez-Quinto F;Ramirez O;Calafell F;Civit S;Lalueza-Fox C
尽管从过去的遗骸中成功地提取了基因组，但由于很难区分污染物和内源DNA序列，人类古基因组学的前景仍然不明朗。以前在高通量测序平台上产生的序列数据表明，古代DNA序列的片段化是一个特征特征，主要是由于脱嘌呤过程产生的基本位点导致DNA断裂。为了研究这种模式是否存在于温带环境的古代遗骸中，我们对5500到49,000年前的不同样本进行了454-FLX焦解测序：来自已灭绝的山羊(Myotragus Balearicus)的一块骨头，经过净化剂(漂白剂)处理的一块骨头，一块未经任何处理的伊比利亚山猫骨头，一块来自巴塞罗那(西班牙)的新石器时代的人类样本，以及一块来自El Sidrón遗址(西班牙阿斯图里亚斯)的尼安德特人的样本。在所有情况下，内源序列的检索效率都低于1%。我们已经使用非人类样本来识别人类序列(分别为0.35%和1.4%)，我们确定这些序列是污染物。我们观察到，漂白剂处理似乎在所产生的污染序列中创建了与脱嘌呤相关的碎片模式，这与先前描述的内源性序列没有区别。此外，在污染物序列的5‘和3’端观察到的核苷酸组成模式比先前在一些尼安德特人污染物中描述的平坦模式要复杂得多。尽管需要对已知污染历史的样本进行大量研究，但我们的结果表明，仅凭碎片模式不能区分内源序列和污染物序列。
Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks. To investigate whether this pattern is present in ancient remains from a temperate environment, we have 454-FLX pyrosequenced different samples dated between 5,500 and 49,000 years ago: a bone from an extinct goat (Myotragus balearicus) that was treated with a depurinating agent (bleach), an Iberian lynx bone not subjected to any treatment, a human Neolithic sample from Barcelona (Spain), and a Neandertal sample from the El Sidrón site (Asturias, Spain). The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, respectively), that we positively know are contaminants. We observed that bleach treatment appears to create a depurination-associated fragmentation pattern in resulting contaminant sequences that is indistinguishable from previously described endogenous sequences. Furthermore, the nucleotide composition pattern observed in 5′ and 3′ ends of contaminant sequences is much more complex than the flat pattern previously described in some Neandertal contaminants. Although much research on samples with known contaminant histories is needed, our results suggest that endogenous and contaminant sequences cannot be distinguished by the fragmentation pattern alone.
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影响因子：
4.5
作者：
Wall JD;Kim SK
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通讯作者：
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