2025/01/01 by Kanako Hisata, Tomofumi Nagata, Megumi Kanai +18 · 1 voice
Environmental Science · Biochemistry, Genetics and Molecular Biology · #Environmental DNA in Biodiversity Studies #Identification and Quantification in Food #Coral and Marine Ecosystems Studies
paper · pdf · doi:10.3755/galaxea.g27d-5
openalex publication_date 2025/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/04
Coral reefs possess the highest biodiversity of all marine ecosystems and zooxanthellate scleractinian corals, the keystone organisms of these reefs, are in crisis due to climate change and anthropogenic activities. Future reef conservation requires comprehensive understanding of the present status of scleractinian taxa in each region. Environmental DNA metabarcoding (eDNA-M) is a method to meet such requirements. Still, it requires optimized primers for PCR amplification of eDNA and complete genomic sequence information for bioinformatic analyses. Coral reefs of Japan reportedly host 85 scleractinian genera. Our previous study developed a primer set that can be used to amplify scleractinian mitochondrial 12S rDNA for eDNA-M analysis. However, at present, the NCBI nucleotide database contains only ~60 genera with available 12S rDNA sequences, indicating that nearly 25 genera that should be detected by this system have no sequence information. To overcome this problem and to establish a nearly complete eDNA-M system for generic level detection of Japanese scleractinians, we collected 22 scleractinian genera and sequenced their mitochondrial genomes. In addition, species of another 12 genera were re-sequenced to avoid sequence differences caused by geographic variation. Incorporation of these data into a newly constructed informatic pipeline resulted in an eDNA-M system that can detect 83 of the 85 genera. This provides a tool for comprehensive, generic level detection of scleractinian corals in Japanese waters.