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

Frontiers in Marine Science

Chuya Shinzato¹  Jun Inoue¹  Haruhi Narisoko²  Noriyuki Satoh²  Koki Nishitsuji²  Tomofumi Nagata³ 

[1] Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan;Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan;Okinawa Environment Science Center, Okinawa, Japan;

关键词: scleractinia;    mitochondrial genome;    primer development;    metabarcoding analyses;    environmental DNA (eDNA);   

DOI  :  10.3389/fmars.2021.758207

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown