New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach
New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach
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DOI：
10.1111/j.1755-0998.2008.02352.x
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发表时间：
2009-01-01
影响因子：
7.7
通讯作者：
Taberlet, Pierre
中科院分区：
文献类型：
--
作者：
Valentini, Alice;Miquel, Christian;Taberlet, Pierre
DNA 条形码（使用标准化 DNA 序列进行物种识别）的发展以及最新 DNA 测序技术的可用性为饮食分析提供了新的可能性。短于 100-150 bp 的 DNA 片段在降解的 DNA 样本中保留的比例要高得多，并且可以从粪便中回收。因此，通过使用通用引物来扩增非常短但信息丰富的 DNA 片段，可以可靠地识别已被食用的植物分类群。根据我们的经验和使用这个识别系统，大约50%的类群可以使用trnL方法识别物种，即使用叶绿体trnL（UAA）内含子的P6环。我们证明了这种新方法快速、易于实施且非常稳健。它可用于大规模的多种植食性物种的饮食分析。我们还证明，我们的方法对于哺乳动物、鸟类、昆虫和软体动物是有效的。这种方法开辟了生态学的新视角，不仅可以进行大规模的饮食研究，还可以加强对竞争物种之间资源分配的研究，并描述生态系统中的食物网。
The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.