Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model
Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model
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DOI：
10.1038/s41598-019-40233-1
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发表时间：
2019-03-05
影响因子：
4.6
通讯作者：
Miya, Masaki
中科院分区：
文献类型：
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作者：
Doi, Hideyuki;Fukaya, Keiichi;Miya, Masaki
环境DNA（eDNA）元条形码是最近开发的一种评估生物多样性的方法，该方法基于对生态系统中存在的DNA进行高通量并行DNA测序。虽然eDNA元条形码可以快速评估生物多样性，但它很容易在野外采样，实验室实验和生物信息学的连续步骤中发生物种检测错误。在这项研究中，我们说明了如何在eDNA metabarcoding为基础的物种检测的错误率可以通过应用多物种占用建模框架。我们报告了一个案例研究与eDNA样本从水族箱中的eDNA元条形码，过滤和PCR的两个主要步骤中的物种的检测概率，在一系列的PCR退火温度，进行了检查。我们还表明，结果可用于检查在给定的实验设计和设置下的物种检测的效率，在物种检测的效率，突出的有用性的多物种网站占用建模框架，研究分子实验的最佳条件。
Environmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and bioinformatics. In this study, we illustrate how the error rates in the eDNA metabarcoding-based species detection can be accounted for by applying the multispecies occupancy modelling framework. We report a case study with the eDNA sample from an aquarium tank in which the detection probabilities of species in the two major steps of eDNA metabarcoding, filtration and PCR, across a range of PCR annealing temperatures, were examined. We also show that the results can be used to examine the efficiency of species detection under a given experimental design and setting, in terms of the efficiency of species detection, highlighting the usefulness of the multispecies site occupancy modelling framework to study the optimum conditions for molecular experiments.