rodent, DNA barcoding, Next Generation Sequencing, Non-invasive samples, Museum samples, Diet
Abstract :
[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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
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
Language :
English
Title :
Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples
Publication date :
2012
Journal title :
PLoS ONE
eISSN :
1932-6203
Publisher :
Public Library of Science, San Franscisco, United States - California
Volume :
7
Issue :
11
Pages :
e48374
Peer reviewed :
Peer Reviewed verified by ORBi
Name of the research project :
Projet innovant du departement EFPA 2011 - www4.inra.fr/efpa/; CERoPath/ANR 07 BDIV 012 - www.ceropath.org/;
Funders :
INRA - Institut National de la Recherche Agronomique [FR] ANR - Agence Nationale de la Recherche [FR] F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
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