Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens

Uchii, Kimiko; Wakimura, Kei; Kikko, Takeshi; Yonekura, Ryuji; Kawaguchi, Riho; Komada, Honoka; Yamanaka, Hiroki; Kenzaka, Takehiko; Tani, Katsuji

doi:10.1007/s10201-021-00665-z

Cited by 3 publications

(7 citation statements)

References 26 publications

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“…Water sampling was conducted during the spawning season of G. caerulescens to obtain high concentrations of eDNA (Uchii et al, 2022) in the southern region (IH, TJ, AK, and SN) and around the Ibanaiko and Nishinoko lagoons, which are located in the eastern region (IB1, IB2, NS1, NS2, and YM) and in the northern region (EN, AM, HR, and MT) (Figure 1). Sampling was performed from April to June 2021 and from March to June 2022, at least twice at each site, but three to five times at most of the sites (Table 1, Table S2).…”

Section: Methodsmentioning

confidence: 99%

“…We sampled 1–2 L of surface water (0–50 cm in depth) using multiple casts (≥5 times) in disposable plastic bags to which benzalkonium chloride solution (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) was added to a final concentration of 0.01% to prevent DNA degradation (Yamanaka et al, 2017). Water samples were filtered on‐site onto a Millipore Sterivex‐HV 0.45 μm sterile filter unit (Merck, Darmstadt, Germany) using a peristaltic pump, as described by Uchii et al (2022). The volumes of filtered water depended on the conditions of samples and were between 0.3 L and 1 L but mostly 0.5 L or 0.6 L (Table S2).…”

Section: Methodsmentioning

confidence: 99%

“…All equipment used for sample collection and filtration, except disposable consumables, was carefully bleached before use. Total DNA was extracted from the filter unit using a DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany), according to the method described by Uchii et al (2022). When eluting DNA from the columns, 50 μL of buffer AE was used to obtain concentrated DNA samples.…”

Section: Methodsmentioning

confidence: 99%

“…Either of the following sets of primers was used to amplify a partial sequence of the CytB gene, including the HTS target region: GcaF and H15915 (Aoyama et al, 2000), or GcCytB_F1 (Uchii et al, 2022) and H15915. PCR products were processed using illustra ExoProStar (Cytiva, Marlborough, MA, USA) and sequenced using the H15915…”

Section: Genetic Evaluation Of G Caerulescens Populations Using Tradi...mentioning

confidence: 99%

“…the field samples, HTS analysis was performed as described in the previous section "HTS library preparation and filtering procedures" with some exceptions. Prior to library preparation for HTS, the concentration of G. caerulescens DNA in each eDNA sample was quantified by real-time PCR targeting a 194-bp partial CytB region(Uchii et al, 2022). Real-time PCR reactions were performed in triplicate with serial dilutions of standard DNA(20,000, 2000, 200, 20, and 2 copies/reaction).…”

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confidence: 99%

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Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

2023

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Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Genetic Evaluation Of G Caerulescens Populations Using Tradi...mentioning

confidence: 99%

mentioning

confidence: 99%

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Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

2023

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Tracking the tropical aquatic dragon: environmental DNA (eDNA) detection for monitoring the endangered Asian arowana, Scleropages formosus (Müller and Schlegel, 1840)

Alshari,

Adnan,

Zainal Abidin

et al. 2024

Hydrobiologia

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An Optimized Environmental DNA Method to Improve Detectability of the Endangered Sichuan Taimen (Hucho bleekeri)

Deng

Zhang

Wang

et al. 2023

Fishes

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Environmental DNA (eDNA) techniques have emerged as a cost-effective and non-invasive strategy for monitoring the distribution of endangered aquatic species. Despite their numerous advantages, operational uncertainty at each step of the process represents a significant challenge that can impact the reliability of results. Hence, the optimization of the eDNA analytic protocol is of utmost importance. In this study, the rare and endangered fish species Sichuan taimen was chosen as the target species to evaluate the concordance between different approaches (tissue, pond, and field water samples) for eDNA detection. The results showed that membrane filtration, collection of a 2-L water sample, and utilization of the DNeasy Tissue and Blood DNA extraction kit were suitable for the analysis of DNA in water samples. Furthermore, the mtDNA D-loop region demonstrated potential as a specific molecular marker for the precise identification of Sichuan taimen. Our results indicated that TaqMan fluorescence PCR can serve as the optimal detection method for reliable identification of target DNA even at extremely low concentrations in the field. This study established an optimized eDNA analysis protocol for Sichuan taimen detection, which will provide the basis for future resource investigations aimed at protection of this endangered aquatic species.

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Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens

Cited by 3 publications

References 26 publications

Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation

Tracking the tropical aquatic dragon: environmental DNA (eDNA) detection for monitoring the endangered Asian arowana, Scleropages formosus (Müller and Schlegel, 1840)

An Optimized Environmental DNA Method to Improve Detectability of the Endangered Sichuan Taimen (Hucho bleekeri)

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