Mar 3, 2017

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

BioRxiv : the Preprint Server for Biology
Masayuki UshioMichio Kondoh

Abstract

In the present study, we added internal standard DNAs (i.e., quantified short DNA fragments from fish species that have never been observed in a sampling area) to environmental DNA (eDNA) samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Japan (from April 2015 to March 2016), and performed metabarcoding analysis to identify fish species and quantify fish eDNA copy number simultaneously. A standard curve was drawn for each sample using the number of reads and the added amount of the standard DNA, which was used to convert the reads of eDNA to the copy numbers. The converted copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled the quantification of eDNA as accurately as quantitative PCR. Furthermore, for samples that show a high level of PCR inhibition, eDNA metabarcoding with internal standard DNAs might allow more accurate quantification than qPCR because the standard curves drawn for internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced 70 quantitative fish eDNA time series in our study, showing that our method would contribute to more ef...Continue Reading

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Mentioned in this Paper

Real-Time Polymerase Chain Reaction
Study
Environment
Sequencing
Zebrafish
Monitoring - Action
Metabolic Inhibition
DNA Binding Domain
probe gene fragment
Species

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