Skip to main content
Dryad logo

Data from: Compared with conventional PCR assay, qPCR assay greatly improves the detection efficiency of predation

Citation

Yang, Ting-bang; Liu, Jie; Chen, Jian (2021), Data from: Compared with conventional PCR assay, qPCR assay greatly improves the detection efficiency of predation, Dryad, Dataset, https://doi.org/10.5061/dryad.1rn8pk0qz

Abstract

Studies of predation can contribute greatly to understanding predator-prey relationships and can also provide integral knowledge concerning food webs and multi-trophic level interactions. Both conventional polymerase chain reaction (cPCR) and quantitative PCR (qPCR) have been employed to detect predation in the field because of their sensitivity and reproducibility. However, to date, few studies have been used to comprehensively demonstrate which method is more sensitive and reproducible in studies of predation. We used a Drosophila melanogaster-specific DNA fragment (99 bp) to construct a tenfold gradient dilution of standards. Additionally, we obtained DNA samples from Pardosa pseudoannulata individuals that fed on D. melanogaster at various time since feeding. Finally, we compared the sensitivity and reproducibility between cPCR and qPCR assays for detecting DNA samples from feeding trials and standards. The results showed that the cPCR and qPCR assay could detect as few as 1.62×103 and 1.62×101 copies of the target DNA fragment, respectively. The cPCR assay could detect as few as 48 h post-feeding of the target DNA fragment. But the qPCR assay showed that all spiders were positive after consuming prey at various time intervals (0, 24, 48, 72 and 96 h). A smaller proportion of the technical replicates were positive using cPCR and some bands on the agarose gel were absent or grey, while some were white and bright for the same DNA samples after amplification by cPCR. By contrast, a larger proportion of the technical replicates were positive using qPCR and the coefficients of variation of the Ct value for the three technical replicates of each DNA sample were less than 5%. These data showed that qPCR was more sensitive and highly reproducible in detecting such degraded DNA from predator’s gut. The present study provides an example of the use of cPCR and qPCR to detect the target DNA fragment of prey remains in predator’s gut.

Usage Notes

The raw data of the sensitivity and reproducibility of TaqMan qPCR. The assay was evaluated using DNA of adult female P. pseudoannulata individuals at various time periods after the consumption of three adult D. melanogaster  and a tenfold gradient dilution of standards ranging from 1.62 × 109 to 1.62 × 100 copies/μL.

Funding

National Natural Science Foundation of China, Award: 31172113

Doctoral Research Startup Foundation of China West Normal University, Award: 412762

Doctoral Research Startup Foundation of China West Normal University, Award: 412762