An in silico approach for the evaluation of DNA barcodes.
An in silico approach for the evaluation of DNA barcodes.
复制标题
DOI：
10.1186/1471-2164-11-434
复制
发表时间：
2010-07-16
期刊：
影响因子：
4.4
通讯作者：
Pompanon F
中科院分区：
文献类型：
--
作者：
Ficetola GF;Coissac E;Zundel S;Riaz T;Shehzad W;Bessière J;Taberlet P;Pompanon F
DNA条形码是生物分类学和环境研究中评估生物多样性的重要工具。条形码的基本特征包括它们对广泛的分类群的适用性以及它们识别甚至密切相关的物种的能力。已经提出了几个DNA区域作为条形码，并且所选择的区域强烈影响研究的输出。然而，到目前为止，条形码之间的正式比较仍然有限。在这里，我们提出了一个标准的方法来评估条形码的质量，基于使用一种新的生物信息学工具，在大型数据库中进行计算机PCR。我们通过比较已经提出的脊椎动物条形码的几个DNA区域的分类覆盖率和分辨率来说明这种方法。为了评估计算机和体外PCR之间的关系，我们还开发了扩增不同种类猫科动物的特异性引物，并使用两种PCR对它们进行了测试。然而，计算机模拟和体外PCR的结果可能会有所不同，这也是因为调整PCR条件可以提高具有有限分类覆盖率的引物的性能。DNA条形码的计算机模拟评估显示分类覆盖率的强烈变化（即，通用性）：基于高度简并引物的条形码和对应于Cyt-b保守区域的条形码显示最高覆盖度。正如预期的那样，较长的条形码比较短的条形码具有更好的分辨率，然而，这对于分析环境样品的生态研究更方便。计算机模拟PCR可用于提高研究的性能，通过允许对几个DNA区域进行初步比较，以根据研究目的确定最合适的条形码。
DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.
登录
查看更多内容
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.1471-8286.2006.01428.x
发表时间：
2006-12-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Ivanova, Natalia V.;Dewaard, Jeremy R.;Hebert, Paul D. N.
通讯作者：
Hebert, Paul D. N.
影响因子：
6.1
作者：
Pegard, Anthony;Miquel, Christian;Pompanon, Francois
通讯作者：
Pompanon, Francois
DOI：
10.1098/rspb.2006.3540
发表时间：
2006-08-22
影响因子：
4.7
作者：
Barber, Paul;Boyce, Sarah L.
通讯作者：
Boyce, Sarah L.
全新世和更新世沉积物中多样的动植物遗传记录
影响因子：
56.9
作者：
Willerslev, E;Hansen, AJ;Cooper, A
通讯作者：
Cooper, A