Title: Towards plant species identification in complex samples: a bioinformatics pipeline for the identification of novel nuclear barcode candidates
Authors: ANGERS ALEXANDREPETRILLO MAUROPARACCHINI VALENTINAKAGKLI DAFNI MARIARISCHITOR PATRICIA ELENAPUERTAS GALLARDO AntonioPATAK DENNSTEDT AlexandreQUERCI MaddalenaKREYSA JOACHIM
Citation: PLOS ONE vol. 11 no. 1 p. e0147692
Publisher: PUBLIC LIBRARY SCIENCE
Publication Year: 2016
JRC N°: JRC96516
ISSN: 1932-6203
URI: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147692
http://publications.jrc.ec.europa.eu/repository/handle/JRC96516
DOI: 10.1371/journal.pone.0147692
Type: Articles in periodicals and books
Abstract: Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.
JRC Directorate:Institute for Health and Consumer Protection Historical Collection

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