Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)

Abstract Many studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical m...

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Autores principales:	Kazutoshi Yoshitake, Atushi Fujiwara, Aiko Matsuura, Masashi Sekino, Motoshige Yasuike, Yoji Nakamura, Reiichiro Nakamichi, Masaaki Kodama, Yumiko Takahama, Akinori Takasuka, Shuichi Asakawa, Kazuomi Nishikiori, Takanori Kobayashi, Shugo Watabe
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/eca9fc4339e04cf4a6e4c89e96cfb8b3
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spelling	oai:doaj.org-article:eca9fc4339e04cf4a6e4c89e96cfb8b32021-12-02T14:26:19ZEstimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)10.1038/s41598-021-86190-62045-2322https://doaj.org/article/eca9fc4339e04cf4a6e4c89e96cfb8b32021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86190-6https://doaj.org/toc/2045-2322Abstract Many studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical method called HaCeD-Seq (Haplotype Count from eDNA), which focuses on the mitochondrial D-loop sequence. The D-loop is a rapidly evolving sequence and has been used to estimate the abundance of eel species in breeding water. In the current study, we have further improved this method by applying unique molecular identifier (UMI) tags, which eliminate the PCR and sequencing errors and extend the detection range by an order of magnitude. Based on this improved HaCeD-Seq pipeline, we computed the abundance of Pacific bluefin tuna (Thunnus orientalis) in aquarium tanks at the Tokyo Sea Life Park (Kasai, Tokyo, Japan). This tuna species is commercially important but is at high risk of resource depletion. With the developed UMI tag method, 90 out of 96 haplotypes (94%) were successfully detected from Pacific bluefin tuna eDNA. By contrast, only 29 out of 96 haplotypes (30%) were detected when UMI tags were not used. Our findings indicate the potential for conducting non-invasive fish stock surveys by sampling eDNA.Kazutoshi YoshitakeAtushi FujiwaraAiko MatsuuraMasashi SekinoMotoshige YasuikeYoji NakamuraReiichiro NakamichiMasaaki KodamaYumiko TakahamaAkinori TakasukaShuichi AsakawaKazuomi NishikioriTakanori KobayashiShugo WatabeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kazutoshi Yoshitake Atushi Fujiwara Aiko Matsuura Masashi Sekino Motoshige Yasuike Yoji Nakamura Reiichiro Nakamichi Masaaki Kodama Yumiko Takahama Akinori Takasuka Shuichi Asakawa Kazuomi Nishikiori Takanori Kobayashi Shugo Watabe Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
description	Abstract Many studies have investigated the ability to identify species from environmental DNA (eDNA). However, even when individual species are identified, the accurate estimation of their abundances by traditional eDNA analyses has been still difficult. We previously developed a novel analytical method called HaCeD-Seq (Haplotype Count from eDNA), which focuses on the mitochondrial D-loop sequence. The D-loop is a rapidly evolving sequence and has been used to estimate the abundance of eel species in breeding water. In the current study, we have further improved this method by applying unique molecular identifier (UMI) tags, which eliminate the PCR and sequencing errors and extend the detection range by an order of magnitude. Based on this improved HaCeD-Seq pipeline, we computed the abundance of Pacific bluefin tuna (Thunnus orientalis) in aquarium tanks at the Tokyo Sea Life Park (Kasai, Tokyo, Japan). This tuna species is commercially important but is at high risk of resource depletion. With the developed UMI tag method, 90 out of 96 haplotypes (94%) were successfully detected from Pacific bluefin tuna eDNA. By contrast, only 29 out of 96 haplotypes (30%) were detected when UMI tags were not used. Our findings indicate the potential for conducting non-invasive fish stock surveys by sampling eDNA.
format	article
author	Kazutoshi Yoshitake Atushi Fujiwara Aiko Matsuura Masashi Sekino Motoshige Yasuike Yoji Nakamura Reiichiro Nakamichi Masaaki Kodama Yumiko Takahama Akinori Takasuka Shuichi Asakawa Kazuomi Nishikiori Takanori Kobayashi Shugo Watabe
author_facet	Kazutoshi Yoshitake Atushi Fujiwara Aiko Matsuura Masashi Sekino Motoshige Yasuike Yoji Nakamura Reiichiro Nakamichi Masaaki Kodama Yumiko Takahama Akinori Takasuka Shuichi Asakawa Kazuomi Nishikiori Takanori Kobayashi Shugo Watabe
author_sort	Kazutoshi Yoshitake
title	Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
title_short	Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
title_full	Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
title_fullStr	Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
title_full_unstemmed	Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)
title_sort	estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted haced-seq (haplotype count from edna)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/eca9fc4339e04cf4a6e4c89e96cfb8b3
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Estimation of tuna population by the improved analytical pipeline of unique molecular identifier-assisted HaCeD-Seq (haplotype count from eDNA)

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