title: Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates.
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.
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Angers-Loustau
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Mauro
authors.initials: M
authors.lastname: Petrillo
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Paracchini
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Dafni M
authors.initials: DM
authors.lastname: Kagkli
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Patricia E
authors.initials: PE
authors.lastname: Rischitor
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Puertas Gallardo
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Patak
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Maddalena
authors.initials: M
authors.lastname: Querci
authors.affiliation: Molecular Biology and Genomic Unit, Institute for Health and Consumer Protection, Joint Research Center, European Commission, Ispra, Italy.
authors.forename: Joachim
authors.initials: J
authors.lastname: Kreysa
mesh_terms: D019295:Computational Biology; D058893:DNA Barcoding, Taxonomic; D017931:DNA Primers / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D010944:Plants / Q000235:genetics
chemical_list: D017931:DNA Primers; D018744:DNA, Plant