Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding

Coral reefs, the most biodiverse habitats in the ocean, are formed by anthozoan cnidarians, the scleractinian corals. Recently, however, ongoing climate change has imperiled scleractinian corals and coral reef environments are changing drastically. Thus, convenient, high-density monitoring of sclera...

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Autores principales:	Chuya Shinzato, Haruhi Narisoko, Koki Nishitsuji, Tomofumi Nagata, Noriyuki Satoh, Jun Inoue
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	scleractinia mitochondrial genome primer development metabarcoding analyses environmental DNA (eDNA) Science Q General. Including nature conservation, geographical distribution QH1-199.5
Acceso en línea:	https://doaj.org/article/c1a2ab069bc849c0b0f23597abc3943c
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spelling	oai:doaj.org-article:c1a2ab069bc849c0b0f23597abc3943c2021-12-01T18:22:05ZNovel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding2296-774510.3389/fmars.2021.758207https://doaj.org/article/c1a2ab069bc849c0b0f23597abc3943c2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmars.2021.758207/fullhttps://doaj.org/toc/2296-7745Coral reefs, the most biodiverse habitats in the ocean, are formed by anthozoan cnidarians, the scleractinian corals. Recently, however, ongoing climate change has imperiled scleractinian corals and coral reef environments are changing drastically. Thus, convenient, high-density monitoring of scleractinian corals is essential to understand changes in coral reef communities. Environmental DNA (eDNA) metabarcoding is potentially one of the most effective means of achieving it. Using publicly available scleractinian mitochondrial genomes, we developed high-specificity primers to amplify mitochondrial 12S ribosomal RNA (12S) and cytochrome oxidase-1 (CO1) genes of diverse scleractinian corals, which could be used for genus-level metabarcoding analyses, using next-generation sequencing technologies. To confirm the effectiveness of these primers, PCR amplicon sequencing was performed using eDNA isolated along the seashore of Okinawa, Japan. We successfully amplified all eDNA samples using PCR. Approximately 93 and 72% of PCR amplicon sequences of 12S and CO1 primers originated from scleractinian 12S and CO1 genes, respectively, confirming higher specificities for coral mitochondrial genes than primers previously used for coral eDNA metabarcoding. We also found that hierarchical clustering, based on the percentage of mapped reads to each scleractinian genus, discriminates between sampling locations, suggesting that eDNA surveys are sufficiently powerful to reveal differences between coral communities separated by <1 km. We conclude that the method reported here is a powerful tool for conducting efficient eDNA surveys targeting scleractinian corals.Chuya ShinzatoHaruhi NarisokoKoki NishitsujiTomofumi NagataNoriyuki SatohJun InoueFrontiers Media S.A.articlescleractiniamitochondrial genomeprimer developmentmetabarcoding analysesenvironmental DNA (eDNA)ScienceQGeneral. Including nature conservation, geographical distributionQH1-199.5ENFrontiers in Marine Science, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	scleractinia mitochondrial genome primer development metabarcoding analyses environmental DNA (eDNA) Science Q General. Including nature conservation, geographical distribution QH1-199.5
spellingShingle	scleractinia mitochondrial genome primer development metabarcoding analyses environmental DNA (eDNA) Science Q General. Including nature conservation, geographical distribution QH1-199.5 Chuya Shinzato Haruhi Narisoko Koki Nishitsuji Tomofumi Nagata Noriyuki Satoh Jun Inoue Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
description	Coral reefs, the most biodiverse habitats in the ocean, are formed by anthozoan cnidarians, the scleractinian corals. Recently, however, ongoing climate change has imperiled scleractinian corals and coral reef environments are changing drastically. Thus, convenient, high-density monitoring of scleractinian corals is essential to understand changes in coral reef communities. Environmental DNA (eDNA) metabarcoding is potentially one of the most effective means of achieving it. Using publicly available scleractinian mitochondrial genomes, we developed high-specificity primers to amplify mitochondrial 12S ribosomal RNA (12S) and cytochrome oxidase-1 (CO1) genes of diverse scleractinian corals, which could be used for genus-level metabarcoding analyses, using next-generation sequencing technologies. To confirm the effectiveness of these primers, PCR amplicon sequencing was performed using eDNA isolated along the seashore of Okinawa, Japan. We successfully amplified all eDNA samples using PCR. Approximately 93 and 72% of PCR amplicon sequences of 12S and CO1 primers originated from scleractinian 12S and CO1 genes, respectively, confirming higher specificities for coral mitochondrial genes than primers previously used for coral eDNA metabarcoding. We also found that hierarchical clustering, based on the percentage of mapped reads to each scleractinian genus, discriminates between sampling locations, suggesting that eDNA surveys are sufficiently powerful to reveal differences between coral communities separated by <1 km. We conclude that the method reported here is a powerful tool for conducting efficient eDNA surveys targeting scleractinian corals.
format	article
author	Chuya Shinzato Haruhi Narisoko Koki Nishitsuji Tomofumi Nagata Noriyuki Satoh Jun Inoue
author_facet	Chuya Shinzato Haruhi Narisoko Koki Nishitsuji Tomofumi Nagata Noriyuki Satoh Jun Inoue
author_sort	Chuya Shinzato
title	Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
title_short	Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
title_full	Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
title_fullStr	Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
title_full_unstemmed	Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding
title_sort	novel mitochondrial dna markers for scleractinian corals and generic-level environmental dna metabarcoding
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/c1a2ab069bc849c0b0f23597abc3943c
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Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding

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