Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Abstract Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughpu...

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Autores principales:	Ryohei Nakao, Ryutei Inui, Yoshihisa Akamatsu, Masuji Goto, Hideyuki Doi, Shunsuke Matsuoka
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ffb46ddb5faa44fc921435c1570c2425
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spelling	oai:doaj.org-article:ffb46ddb5faa44fc921435c1570c24252021-12-02T18:49:23ZIllumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding10.1038/s41598-021-95360-52045-2322https://doaj.org/article/ffb46ddb5faa44fc921435c1570c24252021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95360-5https://doaj.org/toc/2045-2322Abstract Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.Ryohei NakaoRyutei InuiYoshihisa AkamatsuMasuji GotoHideyuki DoiShunsuke MatsuokaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ryohei Nakao Ryutei Inui Yoshihisa Akamatsu Masuji Goto Hideyuki Doi Shunsuke Matsuoka Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
description	Abstract Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.
format	article
author	Ryohei Nakao Ryutei Inui Yoshihisa Akamatsu Masuji Goto Hideyuki Doi Shunsuke Matsuoka
author_facet	Ryohei Nakao Ryutei Inui Yoshihisa Akamatsu Masuji Goto Hideyuki Doi Shunsuke Matsuoka
author_sort	Ryohei Nakao
title	Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
title_short	Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
title_full	Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
title_fullStr	Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
title_full_unstemmed	Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding
title_sort	illumina iseq 100 and miseq exhibit similar performance in freshwater fish environmental dna metabarcoding
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ffb46ddb5faa44fc921435c1570c2425
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Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

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