Reference : Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, D...
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples
Galan, Maxime [Centre de Biologie pour la Gestion des Populations, INRA > > > >]
Pagès, Marie [Université de Liège - ULiège > Département des sciences de la vie > Génétique >]
Cosson, Jean-François [Centre de Biologie pour la Gestion des Populations, INRA > > > >]
Public Library of Science
Yes (verified by ORBi)
San Franscisco
[en] rodent, DNA barcoding, Next Generation Sequencing, Non-invasive samples, Museum samples, Diet
[en] Rodentia are one of the most diverse orders among mammals, with more than 2,000 species currently described. Species assignation based on morphological data alone can present enormous challenges. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b combined with universal rodent primers was selected as the most discriminatory mini-barcode. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next generation sequencing technologies able to sequence multiple DNAs, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.
Institut National de la Recherche Agronomique [Projet innovant du departement EFPA 2011 -] ; French National Agency for Research [CERoPath/ANR 07 BDIV 012 -] ; MP was funded by a Fonds de la Recherche Scientifique-FNRS fellowship (Belgian Fund for Scientific Research -

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