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Quantitative sequencing enables simultaneous absolute quantification and sequencing of environmental DNA of fish species
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  • Tatsuhiko Hoshino,
  • Ryohei Nakao,
  • Toshifumi Minamoto,
  • Hideyuki Doi
Tatsuhiko Hoshino
Japan Agency for Marine-Earth Science and Technology
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Ryohei Nakao
Yamaguchi University
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Toshifumi Minamoto
Kobe University
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Hideyuki Doi
University of Hyogo
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Abstract

Analysis of biodiversity in natural environments based on environmental DNA (eDNA) has been applied to a wide range of ecosystems and species. The combination of high-throughput sequencing technologies and eDNA analysis is a powerful tool that enables comprehensive non-invasive monitoring of species present in the environment. Quantitative data of the eDNA from each species is essential for understanding species abundance but until recently required individual assays targeting each species. Recently developed quantitative sequencing (qSeq) allows simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. The eDNA extracted from aquaria with five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus) across 4 days was quantified by microfluidic digital PCR using a TaqMan probe and qSeq. The eDNA abundance quantified by qSeq was consistent with dPCR for each fish species at each sampling time. However, the relative abundances of sequences obtained from high throughput sequencing did not follow the same trend as the quantitative analyses, probably due to different PCR amplification efficiencies for each species. The correlation coefficients between qSeq and dPCR were 1.052, 1.074, and 1.114 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA. The application of qSeq to eDNA of other species will provide comprehensive quantitative data that could deepen our knowledge of natural ecosystems.

Peer review status:UNDER REVIEW

01 Apr 2020Submitted to Molecular Ecology Resources
21 Apr 2020Assigned to Editor
21 Apr 2020Submission Checks Completed
26 Apr 2020Reviewer(s) Assigned
19 Jun 2020Review(s) Completed, Editorial Evaluation Pending