Effectiveness of blocking primers and a peptide nucleic acid (PNA) clamp for 18S metabarcoding dietary analysis of herbivorous fish.

Autor: Homma C; The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan., Inokuchi D; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan., Nakamura Y; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan., Uy WH; Institute of Fisheries Research and Development, Mindanao State University at Naawan, Naawan, Misamis Oriental, Philippines., Ohnishi K; The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan.; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan., Yamaguchi H; The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan.; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan., Adachi M; The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan.; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2022 Apr 20; Vol. 17 (4), pp. e0266268. Date of Electronic Publication: 2022 Apr 20 (Print Publication: 2022).
DOI: 10.1371/journal.pone.0266268
Abstrakt: The structure of food webs and carbon flow in aquatic ecosystems can be better understood by studying contributing factors such as the diets of herbivorous fish. Metabarcoding using a high-throughput sequencer has recently been used to clarify prey organisms of various fish except herbivorous fish. Since sequences of predator fish have dominated in sequences obtained by metabarcoding, we investigated a method for suppressing the amplification of fish DNA by using a blocking primer or peptide nucleic acid (PNA) clamp to determine the prey organisms of herbivorous fish. We designed three blocking primers and one PNA clamp that anneal to fish-specific sequences and examined how efficient they were in suppressing DNA amplification in various herbivorous fish. The results showed that the PNA clamp completely suppressed fish DNA amplification, and one of the blocking primers suppressed fish DNA amplification but less efficiently than the PNA clamp. Finally, we conducted metabarcoding using mock community samples as templates to determine whether the blocking primer or the PNA clamp was effective in suppressing fish DNA amplification. The results showed that the PNA clamp suppressed 99.3%-99.9% of fish DNA amplification, whereas the blocking primer suppressed 3.3%-32.9%. Therefore, we propose the application of the PNA clamp for clarifying the prey organisms and food preferences of various herbivorous fish.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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