Mosquitoes on a chip—environmental DNA-based detection of invasive mosquito species using high-throughput real-time PCR

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sednas
A PeerJ Hubs article published on behalf of
Zoological Science

Main article text

 

Introduction

Materials & Methods

Site selection for reference specimen and eDNA analysis

Analysis steps for reference specimen

DNA extraction

Molecular species identification (DNA barcoding)

Analysis steps for eDNA samples

eDNA sampling

eDNA extraction

Real-Time PCR

Preamplification and high-throughput real-time PCR

Target sequence confirmation via M13-tagged primers and Sanger sequencing

Statistics

Results

Assay specificity and sensitivity

eDNA detectability with different filter media and qPCR method

Discussion

Conclusions

Supplemental Information

Measured Ct-values obtained via qPCR and HT-qPCR used for statistical analysis

DOI: 10.7717/peerj.17782/supp-1

BLAST results of primers and probes used in this study

DOI: 10.7717/peerj.17782/supp-2

QQ plot of measured Ct values obtained via qPCR and HT-qPCR for all tested modified mosquito qPCR assays

DOI: 10.7717/peerj.17782/supp-3

qPCR standard curves for Ae. albopictus, Ae. japonicus and Ae. koreicus with LOD and LOQ

DOI: 10.7717/peerj.17782/supp-4

qPCR inhibition results per filter type for Ae. japonicus and Ae. koreicus at site cemetery WI Igstadt

Ct value shifts of ≥ 1 indicate PCR inhibition.

DOI: 10.7717/peerj.17782/supp-5

Observed Ct values as function of filtrated water volume until clogging of Sterivex® filters of Ae. albopictus eDNA samples measured via qPCR (●) and HT-qPCR (■)

DOI: 10.7717/peerj.17782/supp-6

Sample site coordinates, used filter medium and final filtered water volumes (in mL) per individual eDNA sample

DOI: 10.7717/peerj.17782/supp-7

List of reference DNA samples from selected Culicidae members used for assay specificity tests

Tissue-derived DNA was used for in vitro tests. Positive (+) or failed amplification (−) results are provided with obtained Ct values at 10 ng/μ l measured via qPCR analysis.

DOI: 10.7717/peerj.17782/supp-8

Standard curve formula, efficiency, R2 and LOQ/LOD values of all assays measured via qPCR

DOI: 10.7717/peerj.17782/supp-9

Sequences obtained from eDNA M13 sequencing for Ae. albopictus, Ae. japonicus and Ae. koreicus extracted from positive eDNA sampling sites

Letters A or B indicate the biological replicates from which the sequences were obtained.

DOI: 10.7717/peerj.17782/supp-10

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Claudia Wittwer conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Chinhda Sharif conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Isabelle Schöck performed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Sven Klimpel conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The Ct measurements are available in the Supplementary File.

Funding

This work was funded by LOEWE-TBG (funding code LOEWE/1/10/519/03/03.001(0014)/52). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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