an in silico approach for the evaluation of dna barcodes在硅片的方法评估dna条形码.pdfVIP

Ficetola et al. BMC Genomics 2010, 11:434 /1471-2164/11/434 METHODOLOGY ARTICLE Open Access An In silico approach for the evaluation of DNA barcodes 1,2,3*† 1*† 1 1 1 Gentile Francesco Ficetola , Eric Coissac , Stéphanie Zundel , Tiayyba Riaz , Wasim Shehzad , 1 1 1 Julien Bessière , Pierre Taberlet , François Pompanon Abstract Background: 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 Results: 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., univ