In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River.
In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River.
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在对使用Primertree和应用的EDNA研究底漆的计算机评估中，以表征Cuyahoga河周围的生物多样性。
DOI：
10.1038/srep22908
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发表时间：
2016-03-11
影响因子：
4.6
通讯作者：
Serre D
中科院分区：
文献类型：
--
作者：
Cannon MV;Hester J;Shalkhauser A;Chan ER;Logue K;Small ST;Serre D
环境DNA（eDNA）的分析能够从水和土壤样品中检测感兴趣的物种，通常使用物种特异性PCR。在这里，我们描述了一种通过使用针对广泛分类群的引物对扩增eDNA和用于物种识别的高通量测序来表征给定环境生物多样性的方法。我们测试了这种方法上收集沿着凯霍加河（俄亥俄州，美国）的91个水样的40毫升。我们使用12对引物扩增eDNA，靶向哺乳动物，鱼类，两栖动物，鸟类，甲壳类动物，节肢动物，桡足类动物，植物和几种微生物类群，并通过高通量测序同时测序所有PCR产物。总的来说，我们确定了15种鱼类，17种哺乳动物，8种鸟类，15种节肢动物，一种海龟和一种蝾螈的DNA序列。有趣的是，除了水生和半水生动物外，我们还从凯霍加河附近的陆地物种中鉴定了DNA。我们还确定了一个亚洲鲤鱼物种的DNA入侵五大湖，但以前没有在凯霍加河报告。我们的研究表明，使用大范围PCR扩增结合高通量测序从小水样中提取的eDNA分析可以提供生物多样性的广阔前景。
Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semi-aquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.