10.5061/DRYAD.1J6V6
Galan, Maxime
Montpellier SupAgro
Pagès, Marie
Montpellier SupAgro
University of Liège
Cosson, Jean-François
Montpellier SupAgro
Data from: Next-generation sequencing for rodent barcoding: species
identification from fresh, degraded and environmental samples
Dryad
dataset
2013
molecular species identification
Diet Analysis
environmental barcoding
Rodentia
Molecular taxonomy
Next-generation sequencing
2013-02-05T20:37:34Z
2013-02-05T20:37:34Z
en
https://doi.org/10.1371/journal.pone.0048374
12475294 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Rodentia is the most diverse order among mammals, with more than 2,000
species currently described. Most of the time, species assignation is so
difficult based on morphological data solely that identifying rodents at
the specific level corresponds to a real challenge. 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 was selected as the most discriminatory
mini-barcode, and rodent universal primers surrounding this fragment were
designed. 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 mixes of DNA, 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.
Fasta S1 COI115Species from GenBankAlignment of COI sequences from 115
rodent species from GenBankFasta S2 Cytb115Species from GenBankAlignment
of cytb sequences from 115 rodent species from GenBankFasta S3 Design
primersFasta S4 Reference SamplesAlignment of rodent haplotypes obtained
from the 265 reference samplesFasta S5 Rodentia HaplotypesAlignment of the
rodent haplotypes obtained for ethanol preserved samplesFasta S6 Prey
HaplotypesAlignment of the prey haplotypes obtained from faecal and pellet
samplesFasta S7 Museum Murinae True HaplotypesAlignment of the rodent
haplotypes obtained from museum samplesFasta S8 Museum Human DNA
contamination HaplotypesAlignment of the human haplotypes retrieved from
rodent museum sample analysisFasta S9 Museum DNA contamination
HaplotypesAlignment of the vertebrate haplotypes corresponding to
contaminations detected in rodent museum samplesFasta S10 Predator
HaplotypesAlignment of the predator haplotypes detected in faecal and
pellet samplesFatsa S11 Environnemental contamination HaplotypesAlignment
of the bacterial and unknown haplotypes detected in faecal and pellet
samples
West Africa
Europe
China
South-East Asia
East Africa