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タイトル: Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia
著者: Sakata, Masayuki K.
Kawata, Mone U.
Kurabayashi, Atsushi
Kurita, Takaki
Nakamura, Masatoshi
Shirako, Tomoyasu
Kakehashi, Ryosuke
Nishikawa, Kanto  kyouindb  KAKEN_id  orcid https://orcid.org/0000-0002-6274-4959 (unconfirmed)
Hossman, Mohamad Yazid
Nishijima, Takashi
Kabamoto, Junichi
Miya, Masaki
Minamoto, Toshifumi
著者名の別形: 坂田, 雅之
河田, 萌音
倉林, 敦
栗田, 隆気
中村, 匡聡
白子, 智康
掛橋, 竜祐
西川, 完途
西島, 太加志
樺元, 淳一
宮, 正樹
源, 利文
キーワード: Аgricultural ecosystem
Amphibia
biodiversity monitoring
environmental DNA
metabarcoding
universal primer
発行日: 2022
出版者: Pensoft Publishers
誌名: Metabarcoding and Metagenomics
巻: 6
開始ページ: 15
終了ページ: 26
論文番号: e76534
抄録: Biodiversity monitoring is important for the conservation of natural ecosystems in general, but particularly for amphibians, whose populations are pronouncedly declining. However, amphibians’ ecological traits (e.g. nocturnal or aquatic) often prevent their precise monitoring. Environmental DNA (eDNA) metabarcoding – analysis of extra-organismal DNA released into the environment – allows the easy and effective monitoring of the biodiversity of aquatic organisms. Here, we developed and tested the utility of original PCR primer sets. First, we conducted in vitro PCR amplification tests with universal primer candidates using total DNA extracted from amphibian tissues. Five primer sets successfully amplified the target DNA fragments (partial 16S rRNA gene fragments of 160–311 bp) from all 16 taxa tested (from the three living amphibian orders Anura, Caudata and Gymnophiona). Next, we investigated the taxonomic resolution retrieved using each primer set. The results revealed that the universal primer set “Amph16S” had the highest resolution amongst the tested sets. Finally, we applied Amph16S to the water samples collected in the field and evaluated its detection capability by comparing the species detected using eDNA and physical survey (capture-based sampling and visual survey) in multiple agricultural ecosystems across Japan (160 sites in 10 areas). The eDNA metabarcoding with Amph16S detected twice as many species as the physical surveys (16 vs. 8 species, respectively), indicating the effectiveness of Amph16S in biodiversity monitoring and ecological research for amphibian communities.
記述: 水をくむだけの新しい両生類の調査法. 京都大学プレスリリース. 2022-02-22.
著作権等: © 2022 Masayuki K. Sakata, Mone U. Kawata, Atsushi Kurabayashi, Takaki Kurita, Masatoshi Nakamura, Tomoyasu Shirako, Ryosuke Kakehashi, Kanto Nishikawa, Mohamad Yazid Hossman, Takashi Nishijima, Junichi Kabamoto, Masaki Miya, Toshifumi Minamoto.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
URI: http://hdl.handle.net/2433/268026
DOI(出版社版): 10.3897/mbmg.6.76534
関連リンク: https://www.kyoto-u.ac.jp/ja/research-news/2022-02-22
出現コレクション:学術雑誌掲載論文等

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