Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.
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DOI：
10.1371/journal.pone.0017497
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发表时间：
2011-04-13
期刊：
影响因子：
3.7
通讯作者：
Baird DJ
中科院分区：
文献类型：
--
作者：
Hajibabaei M;Shokralla S;Zhou X;Singer GA;Baird DJ
及时和准确的生物多样性分析对生物监测计划的成功构成了持续的挑战。基于形态学的生物指示类群的鉴定是耗时的，并且很少支持物种水平的分辨率，特别是对于未成熟的生命阶段。在过去的十年中，已经做了大量的工作，以开发生物多样性分析的替代方法，使用基于DNA序列的方法，如分子生物学和DNA条形码。正在进行的DNA条形码参考文库的组装将为基于DNA的鉴定系统提供基础。在生物多样性科学中使用最近引入的下一代测序（NGS）方法有可能将DNA信息在常规生物监测应用中的应用进一步扩展到前所未有的规模。在这里，我们证明了使用454个大规模并行焦磷酸测序的生物监测常用的淡水底栖大型无脊椎动物类群的物种水平的分析的可行性。我们设计实验是为了直接比较基于形态学的、桑格测序DNA条形码和下一代环境条形码方法。我们的结果显示了微型条形码的454焦磷酸测序准确鉴定合并混合物中丰度超过1%的所有物种的能力。虽然该方法未能识别混合物中的6个稀有物种，但混合物中未被个体代表的9个物种的序列的存在提供了证据，表明基于DNA的分析可能提供了在大量环境样品中发现稀有物种的有价值的方法。我们进一步展示了应用环境条形码的方法，通过比较从城市地区的底栖大型无脊椎动物的保护区。虽然将需要相当大的努力，强大的优化NGS工具，以确定从散装环境样品的物种，我们的研究结果表明，生物监测计划的环境条形码方法的潜力。
Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.
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影响因子：
5.4
作者：
Hajibabaei M;Singer GA;Clare EL;Hebert PD
通讯作者：
Hebert PD
DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
DOI：
10.1111/j.1471-8286.2007.01678.x
发表时间：
2007-05-01
期刊：
Molecular ecology notes
影响因子：
--
作者：
Ratnasingham S;Hebert PD
通讯作者：
Hebert PD
影响因子：
64.8
作者：
Margulies, M;Egholm, M;Rothberg, JM
通讯作者：
Rothberg, JM
影响因子：
3
作者：
Singer, Gregory A. C.;Hajibabaei, Mehrdad
通讯作者：
Hajibabaei, Mehrdad