Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

Abstract The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in...

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Autores principales:	Tatsuhiko Hoshino, Ryohei Nakao, Hideyuki Doi, Toshifumi Minamoto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/32244f375d184f17ac1a11d059f9dce5
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spelling	oai:doaj.org-article:32244f375d184f17ac1a11d059f9dce52021-12-02T10:59:18ZSimultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique10.1038/s41598-021-83318-62045-2322https://doaj.org/article/32244f375d184f17ac1a11d059f9dce52021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83318-6https://doaj.org/toc/2045-2322Abstract The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables 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. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.Tatsuhiko HoshinoRyohei NakaoHideyuki DoiToshifumi MinamotoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tatsuhiko Hoshino Ryohei Nakao Hideyuki Doi Toshifumi Minamoto Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
description	Abstract The combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables 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. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.
format	article
author	Tatsuhiko Hoshino Ryohei Nakao Hideyuki Doi Toshifumi Minamoto
author_facet	Tatsuhiko Hoshino Ryohei Nakao Hideyuki Doi Toshifumi Minamoto
author_sort	Tatsuhiko Hoshino
title	Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
title_short	Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
title_full	Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
title_fullStr	Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
title_full_unstemmed	Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
title_sort	simultaneous absolute quantification and sequencing of fish environmental dna in a mesocosm by quantitative sequencing technique
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/32244f375d184f17ac1a11d059f9dce5
work_keys_str_mv	AT tatsuhikohoshino simultaneousabsolutequantificationandsequencingoffishenvironmentaldnainamesocosmbyquantitativesequencingtechnique AT ryoheinakao simultaneousabsolutequantificationandsequencingoffishenvironmentaldnainamesocosmbyquantitativesequencingtechnique AT hideyukidoi simultaneousabsolutequantificationandsequencingoffishenvironmentaldnainamesocosmbyquantitativesequencingtechnique AT toshifumiminamoto simultaneousabsolutequantificationandsequencingoffishenvironmentaldnainamesocosmbyquantitativesequencingtechnique
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Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

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