Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the Northern Red Sea

High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the Northern Red Sea. Samples were obtained from standardized sampling devices [Autonomous Reef Monitoring Structures (ARMS)] deployed for 18 months. DNA barcoding of non-sessile specimens >2mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2mm-500μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest ...