TY - JOUR
T1 - Towards plant species identification in complex samples
T2 - A bioinformatics pipeline for the identification of novel nuclear barcode candidates
AU - Angers-Loustau, Alexandre
AU - Petrillo, Mauro
AU - Paracchini, Valentina
AU - Kagkli, Dafni M.
AU - Rischitor, Patricia E.
AU - Gallardo, Antonio Puertas
AU - Patak, Alex
AU - Querci, Maddalena
AU - Kreysa, Joachim
PY - 2016/1/1
Y1 - 2016/1/1
N2 - 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.
AB - 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.
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U2 - 10.1371/journal.pone.0147692
DO - 10.1371/journal.pone.0147692
M3 - Article
AN - SCOPUS:84958191328
SN - 1932-6203
VL - 11
JO - PLoS One
JF - PLoS One
IS - 1
M1 - e0147692
ER -