RT Journal Article
SR Electronic
T1 Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 113472
DO 10.1101/113472
A1 Masayuki Ushio
A1 Hiroaki Murakami
A1 Reiji Masuda
A1 Tetsuya Sado
A1 Masaki Miya
A1 Sho Sakurai
A1 Hiroki Yamanaka
A1 Toshifumi Minamoto
A1 Michio Kondoh
YR 2017
UL http://biorxiv.org/content/early/2017/03/05/113472.abstract
AB 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 efficient and quantitative monitoring of biodiversity.