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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doaj-ffb46ddb5faa44fc921435c1570c24252021-08-08T11:23:55ZengNature Publishing GroupScientific Reports2045-23222021-08-0111111010.1038/s41598-021-95360-5Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcodingRyohei Nakao0Ryutei Inui1Yoshihisa Akamatsu2Masuji Goto3Hideyuki Doi4Shunsuke Matsuoka5Graduate School of Science and Technology for Innovation, Yamaguchi UniversityFaculty of Socio-Environmental Studies, Fukuoka Institute of TechnologyGraduate School of Science and Technology for Innovation, Yamaguchi UniversityResearch and Development Center of Nippon Koei Co. Ltd.Graduate School of Simulation Studies, University of HyogoGraduate School of Simulation Studies, University of HyogoAbstract 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.https://doi.org/10.1038/s41598-021-95360-5 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ryohei Nakao Ryutei Inui Yoshihisa Akamatsu Masuji Goto Hideyuki Doi Shunsuke Matsuoka |
spellingShingle |
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 Scientific Reports |
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 Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2021-08-01 |
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. |
url |
https://doi.org/10.1038/s41598-021-95360-5 |
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