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Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called H...

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Autores principales: Yoshitake, Kazutoshi, Yanagisawa, Kyohei, Sugimoto, Yuma, Nakamura, Hiroshi, Mizusawa, Nanami, Miya, Masaki, Hamasaki, Koji, Kobayashi, Takanori, Watabe, Shugo, Nishikiori, Kazuomi, Asakawa, Shuichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10033627/
https://www.ncbi.nlm.nih.gov/pubmed/36947319
http://dx.doi.org/10.1007/s10142-023-01013-3
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author Yoshitake, Kazutoshi
Yanagisawa, Kyohei
Sugimoto, Yuma
Nakamura, Hiroshi
Mizusawa, Nanami
Miya, Masaki
Hamasaki, Koji
Kobayashi, Takanori
Watabe, Shugo
Nishikiori, Kazuomi
Asakawa, Shuichi
author_facet Yoshitake, Kazutoshi
Yanagisawa, Kyohei
Sugimoto, Yuma
Nakamura, Hiroshi
Mizusawa, Nanami
Miya, Masaki
Hamasaki, Koji
Kobayashi, Takanori
Watabe, Shugo
Nishikiori, Kazuomi
Asakawa, Shuichi
author_sort Yoshitake, Kazutoshi
collection PubMed
description Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10142-023-01013-3.
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spelling pubmed-100336272023-03-24 Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers Yoshitake, Kazutoshi Yanagisawa, Kyohei Sugimoto, Yuma Nakamura, Hiroshi Mizusawa, Nanami Miya, Masaki Hamasaki, Koji Kobayashi, Takanori Watabe, Shugo Nishikiori, Kazuomi Asakawa, Shuichi Funct Integr Genomics Original Article Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10142-023-01013-3. Springer Berlin Heidelberg 2023-03-22 2023 /pmc/articles/PMC10033627/ /pubmed/36947319 http://dx.doi.org/10.1007/s10142-023-01013-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Original Article
Yoshitake, Kazutoshi
Yanagisawa, Kyohei
Sugimoto, Yuma
Nakamura, Hiroshi
Mizusawa, Nanami
Miya, Masaki
Hamasaki, Koji
Kobayashi, Takanori
Watabe, Shugo
Nishikiori, Kazuomi
Asakawa, Shuichi
Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title_full Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title_fullStr Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title_full_unstemmed Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title_short Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers
title_sort pilot study of a comprehensive resource estimation method from environmental dna using universal d-loop amplification primers
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10033627/
https://www.ncbi.nlm.nih.gov/pubmed/36947319
http://dx.doi.org/10.1007/s10142-023-01013-3
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