Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, Grenoble, France.
Mol Ecol. 2012 Apr;21(8):1834-47. doi: 10.1111/j.1365-294X.2012.05550.x.
Almost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under-explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom-made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.
几乎所有生态学的实证研究都必须识别出所研究生态过程中涉及的物种。DNA 条形码技术结合了 DNA 条形码的原理和下一代测序技术，为大量生物多样性数据的产生提供了机会。微生物学家长期以来一直使用代谢条形码方法，但该技术在植物和动物群落生物多样性评估中的应用仍有待探索。尽管它与 DNA 条形码有关，但 DNA 代谢条形码的一些独特特征证明了开发特定数据分析方法的合理性。在这篇综述中，我们描述了可用于动植物 DNA 代谢条形码的生物信息学工具，并重新讨论了为 DNA 条形码或微生物代谢条形码开发的其他工具。我们还讨论了在 DNA 代谢条形码背景下评估和比较 DNA 条形码的原则和相关工具，用于设计新的定制条形码以适应特定的生态问题，用于处理 PCR 和测序错误，以及用于从序列中推断分类学数据。
