Data from: Improving PCR detection of prey in molecular diet studies: importance of group-specific primer set selection and extraction protocol performances ...
While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the p...
| Main Authors: | , , |
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| Format: | Dataset |
| Language: | English |
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Dryad
2012
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.5061/dryad.8c134 https://datadryad.org/stash/dataset/doi:10.5061/dryad.8c134 |
| Summary: | While morphological identification of prey remains in feces of predators is the method most commonly used to study trophic interactions, many studies indicate that this method does not detect all consumed prey. Polymerase Chain Reaction based methods are increasingly used to detect prey DNA in the predator food bolus and have proved themselves efficient, with high accuracy. When studying complex diet samples, the extraction of total DNA is a critical step, as PCR inhibitors may be co-extracted. Another critical step consist in carefully select suitable group-specific primer sets that should only amplify prey DNA from the targeted taxon. In this study, the food boluses of five Rattus rattus and seven Rattus exulans were analyzed using both morphological and molecular methods. We tested a panel of 30 PCR specific primer sets targeting Bird, Invertebrate and Plant sequences and four were finally selected to be use as group-specific primer pairs in PCR protocols. The performances of four DNA extraction protocols ... : Alignment of group-specific primer set regionsSequence alignment of DNA regions targeted by the four group-specific primer pairs amplifying Bird, Invertebrate and Plant (mitochondrial and chloroplastic) DNA. Target and non target species were aligned for each group-specific primer pair. Target species were chosen to be as much as possible divergent in order to highlight the potentiality of each primer pair to amplify a wide prey diversity. "N" represents unavailable nucleotide in the existing Genbank sequence, "-" indicates gap and nucleotides between brackets indicate insertions. Note that because Animals do not have chloraplastic DNA, only sequences from target species were aligned for the Plant chloroplastic primer pair. ... |
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